Mercurial > repos > galaxyp > msi_qualitycontrol
annotate msi_qualitycontrol.xml @ 10:3eee933c27cf draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
author | galaxyp |
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date | Tue, 19 Jun 2018 18:08:15 -0400 |
parents | 963c7ec00141 |
children | 30d0aabb1b46 |
rev | line source |
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10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.2"> |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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2 <description> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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3 mass spectrometry imaging QC |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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4 </description> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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5 <requirements> |
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52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
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1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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9 <requirement type="package" version="2.2.1">r-gridextra</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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11 <requirement type="package" version="0.5.0">r-scales</requirement> |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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12 </requirements> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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13 <command detect_errors="exit_code"> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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14 <![CDATA[ |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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15 #if $infile.ext == 'imzml' |
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52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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16 ln -s '${infile.extra_files_path}/imzml' infile.imzML && |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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17 ln -s '${infile.extra_files_path}/ibd' infile.ibd && |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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18 #elif $infile.ext == 'analyze75' |
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52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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19 ln -s '${infile.extra_files_path}/hdr' infile.hdr && |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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20 ln -s '${infile.extra_files_path}/img' infile.img && |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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21 ln -s '${infile.extra_files_path}/t2m' infile.t2m && |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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22 #else |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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23 ln -s '$infile' infile.RData && |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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24 #end if |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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25 cat '${cardinal_qualitycontrol_script}' && |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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26 Rscript '${cardinal_qualitycontrol_script}' |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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27 ]]> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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28 </command> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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29 <configfiles> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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30 <configfile name="cardinal_qualitycontrol_script"><![CDATA[ |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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31 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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32 ################################# load libraries and read file ################# |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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33 |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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34 library(Cardinal) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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35 library(ggplot2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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36 library(RColorBrewer) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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37 library(gridExtra) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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38 library(KernSmooth) |
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3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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39 library(scales) |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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40 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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41 #if $infile.ext == 'imzml' |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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42 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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43 #elif $infile.ext == 'analyze75' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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44 msidata = readAnalyze('infile') |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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45 #else |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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46 load('infile.RData') |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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47 #end if |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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48 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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49 ## create full matrix to make processed imzML files compatible with segmentation |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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50 iData(msidata) <- iData(msidata)[] |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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51 |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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52 ###################################### file properties in numbers ###################### |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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53 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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54 ## Number of features (m/z) |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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55 maxfeatures = length(features(msidata)) |
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963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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56 ## Range m/z |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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57 minmz = round(min(mz(msidata)), digits=2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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58 maxmz = round(max(mz(msidata)), digits=2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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59 ## Number of spectra (pixels) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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60 pixelcount = length(pixels(msidata)) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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61 ## Range x coordinates |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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62 minimumx = min(coord(msidata)[,1]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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63 maximumx = max(coord(msidata)[,1]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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64 ## Range y coordinates |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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65 minimumy = min(coord(msidata)[,2]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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66 maximumy = max(coord(msidata)[,2]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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67 ## Range of intensities |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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68 minint = round(min(spectra(msidata)[]), digits=2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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69 maxint = round(max(spectra(msidata)[]), digits=2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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70 medint = round(median(spectra(msidata)[]), digits=2) |
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1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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71 ## Number of intensities > 0 |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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72 npeaks= sum(spectra(msidata)[]>0) |
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963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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73 ## Spectra multiplied with m/z (potential number of peaks) |
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845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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74 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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75 ## Percentage of intensities > 0 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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76 percpeaks = round(npeaks/numpeaks*100, digits=2) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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77 ## Number of empty TICs |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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78 TICs = colSums(spectra(msidata)[]) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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79 NumemptyTIC = sum(TICs == 0) |
9
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80 ## Median TIC |
10
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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81 medTIC = round(median(TICs), digits=2) |
9
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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82 ## Median peaks per spectrum |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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83 medpeaks = median(colSums(spectra(msidata)[]>0)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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84 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson")) |
0
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85 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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86 ## Processing informations |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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87 processinginfo = processingData(msidata) |
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88 centroidedinfo = processinginfo@centroided |
0
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89 |
9
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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90 ## if TRUE write processinginfo if FALSE write FALSE |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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91 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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92 ## normalization |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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93 if (length(processinginfo@normalization) == 0) { |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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94 normalizationinfo='FALSE' |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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95 } else { |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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96 normalizationinfo=processinginfo@normalization |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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97 } |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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98 ## smoothing |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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99 if (length(processinginfo@smoothing) == 0) { |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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100 smoothinginfo='FALSE' |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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101 } else { |
845073d506a8
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102 smoothinginfo=processinginfo@smoothing |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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103 } |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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104 ## baseline |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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105 if (length(processinginfo@baselineReduction) == 0) { |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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106 baselinereductioninfo='FALSE' |
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107 } else { |
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108 baselinereductioninfo=processinginfo@baselineReduction |
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109 } |
845073d506a8
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110 ## peak picking |
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111 if (length(processinginfo@peakPicking) == 0) { |
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112 peakpickinginfo='FALSE' |
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113 } else { |
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114 peakpickinginfo=processinginfo@peakPicking |
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115 } |
845073d506a8
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116 |
9
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117 ############## Read and filter tabular file with m/z ########################### |
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118 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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119 ### reading peptide file: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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120 |
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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121 #if $peptide_file: |
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122 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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123 input_list = read.delim("$peptide_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE) |
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124 if (ncol(input_list) == 1) |
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125 {input_list = cbind(input_list, input_list)} ## if there is just one column dublicate it to have a names column |
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126 |
9
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127 ### calculate how many input peptide m/z are valid: |
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128 |
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129 inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,] |
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130 number_peptides_in = length(input_list[,1]) |
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131 number_peptides_valid = length(inputpeptides[,1]) |
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132 |
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133 #else |
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134 |
5
ac786240ef07
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135 inputpeptides = as.data.frame(matrix(, nrow = 0, ncol = 2)) |
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136 number_peptides_in = 0 |
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137 number_peptides_valid = 0 |
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138 |
4
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139 #end if |
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140 |
9
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141 colnames(inputpeptides) = c("m/z", "name") |
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142 |
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143 ### reading calibrant file: |
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144 |
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145 #if $calibrant_file: |
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146 |
4
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147 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE) |
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148 if (ncol(calibrant_list) == 1) |
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149 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column |
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150 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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151 ### calculate how many input calibrant m/z are valid: |
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152 |
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153 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,] |
963c7ec00141
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154 number_calibrants_in = length(calibrant_list[,1]) |
963c7ec00141
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155 number_calibrants_valid = length(inputcalibrants[,1]) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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156 |
4
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157 #else |
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158 |
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159 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2)) |
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160 number_calibrants_in = 0 |
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161 number_calibrants_valid = 0 |
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162 |
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163 #end if |
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164 |
9
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165 colnames(inputcalibrants) = c("m/z", "name") |
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166 |
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167 ### bind inputcalibrants and inputpeptides together, to make m/z heatmaps on both |
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168 |
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169 inputs_all = rbind(inputcalibrants[,1:2], inputpeptides[,1:2]) |
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170 inputmasses = inputs_all[,1] |
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171 inputnames = inputs_all[,2] |
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172 |
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173 ######################################## PDF ############################################# |
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174 ########################################################################################## |
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175 ########################################################################################## |
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176 |
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177 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12) |
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178 plot(0,type='n',axes=FALSE,ann=FALSE) |
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179 |
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180 ## if no filename is given, name of file in Galaxy history is used |
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181 |
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182 #if not $filename: |
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183 #set $filename = $infile.display_name |
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184 #end if |
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185 |
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186 title(main=paste("$filename")) |
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187 |
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188 ################# I) file properties in numbers ################################ |
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189 ################################################################################ |
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190 print("properties in numbers") |
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191 |
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192 properties = c("Number of m/z features", |
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193 "Range of m/z values", |
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194 "Number of pixels", |
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195 "Range of x coordinates", |
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196 "Range of y coordinates", |
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197 "Range of intensities", |
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198 "Median of intensities", |
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199 "Intensities > 0", |
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200 "Number of zero TICs", |
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201 "Median TIC", |
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202 "Median # peaks per spectrum", |
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203 "Normalization", |
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204 "Smoothing", |
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205 "Baseline reduction", |
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206 "Peak picking", |
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207 "Centroided", |
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208 paste0("# peptides in \n", "$peptide_file.display_name"), |
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209 paste0("# calibrants in \n", "$calibrant_file.display_name")) |
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210 |
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211 values = c(paste0(maxfeatures), |
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212 paste0(minmz, " - ", maxmz), |
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213 paste0(pixelcount), |
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214 paste0(minimumx, " - ", maximumx), |
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215 paste0(minimumy, " - ", maximumy), |
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216 paste0(minint, " - ", maxint), |
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217 paste0(medint), |
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218 paste0(percpeaks, " %"), |
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219 paste0(NumemptyTIC), |
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220 paste0(medTIC), |
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221 paste0(medpeaks), |
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222 paste0(normalizationinfo), |
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223 paste0(smoothinginfo), |
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224 paste0(baselinereductioninfo), |
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225 paste0(peakpickinginfo), |
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226 paste0(centroidedinfo), |
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227 paste0(number_peptides_valid, " / " , number_peptides_in), |
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228 paste0(number_calibrants_valid, " / ", number_calibrants_in)) |
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229 |
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230 property_df = data.frame(properties, values) |
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231 |
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232 grid.table(property_df, rows= NULL) |
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233 |
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234 ####################### II) images in x-y grid ############################### |
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235 ############################################################################## |
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236 print("x-y images") |
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237 |
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238 if (npeaks > 0){ |
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239 ## function for density plots |
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240 plot_colorByDensity = function(x1,x2, |
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241 ylim=c(min(x2),max(x2)), |
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242 xlim=c(min(x1),max(x1)), |
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243 xlab="",ylab="",main=""){ |
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244 df = data.frame(x1,x2) |
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245 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white"))) |
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246 df\$dens = col2rgb(x)[1,] + 1L |
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247 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256) |
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248 df\$col = cols[df\$dens] |
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249 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col, |
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250 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)} |
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251 |
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252 abline_vector= -100000 ## will be filled for samples in case data is combined |
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253 |
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254 ## start list for optional spectrum values output |
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255 spectrum_list = list() |
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256 list_count = 1 |
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257 |
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258 ################### 0) overview for combined data ########################### |
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259 |
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260 ### only for previously combined data, same plot as in combine QC pdf |
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261 |
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262 if (!is.null(levels(msidata\$combined_sample))){ |
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263 number_combined = length(levels(msidata\$combined_sample)) |
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264 |
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265 ## the more combined_samples a file has the smaller will be the legend |
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266 if (number_combined<20){ |
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267 legend_size = 10 |
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268 cex_boxplot = 1 |
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269 }else if (number_combined>20 && number_combined<40){ |
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270 legend_size = 9 |
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271 cex_boxplot = 0.8 |
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272 }else if (number_combined>40 && number_combined<60){ |
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273 legend_size = 8 |
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274 cex_boxplot = 0.6 |
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275 }else if (number_combined>60 && number_combined<100){ |
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276 legend_size = 7 |
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277 cex_boxplot = 0.5 |
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278 }else{ |
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279 legend_size = 6 |
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280 cex_boxplot = 0.3 |
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281 } |
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282 |
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283 position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample) |
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284 colnames(position_df)[3] = "sample_name" |
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285 |
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286 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ |
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287 geom_tile() + |
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288 coord_fixed()+ |
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289 ggtitle("Spatial orientation of combined data")+ |
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290 theme_bw()+ |
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291 theme(plot.title = element_text(hjust = 0.5))+ |
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292 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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293 theme(legend.position="bottom",legend.direction="vertical")+ |
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294 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ |
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295 guides(fill=guide_legend(ncol=5,byrow=TRUE)) |
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296 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) |
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297 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) |
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298 for(file_count in 1:nrow(coord_labels)) |
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299 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], |
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300 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} |
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301 |
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302 print(combine_plot) |
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303 |
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304 ### find max pixelnumber per subsample to later draw ablines |
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305 pixel_name_df = data.frame(pixels(msidata), msidata\$combined_sample) |
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306 colnames(pixel_name_df) = c("pixel_number", "pixel_name") |
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307 last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max) |
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308 pixel_vector = last_pixel[,2] |
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309 abline_vector = pixel_vector[1:number_combined-1] |
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310 print(abline_vector) |
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311 } |
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312 |
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313 ################### 1) Pixel order image ################################### |
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314 |
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315 pixelnumber = 1:pixelcount |
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316 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber) |
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317 |
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318 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+ |
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319 geom_tile() + coord_fixed()+ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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320 ggtitle("Pixel order") + theme_bw()+ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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321 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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322 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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323 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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324 space = "Lab", na.value = "black", name = "Pixel number")) |
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325 |
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326 ################ 2) Number of calibrants per spectrum ###################### |
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327 |
2
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328 pixelmatrix = matrix(ncol=ncol(msidata), nrow=0) |
1ccbda92b76b
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329 inputcalibrantmasses = inputcalibrants[,1] |
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330 |
9
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331 ### find m/z range (ppm) for each calibrant and extract intensity matrix for this range |
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332 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses |
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333 |
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334 if (length(inputcalibrantmasses) != 0){ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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335 for (calibrantnr in 1:length(inputcalibrantmasses)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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336 calibrantmz = inputcalibrantmasses[calibrantnr] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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337 calibrantfeaturemin = features(msidata, mz=calibrantmz-plusminusvalues[calibrantnr]) |
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338 calibrantfeaturemax = features(msidata, mz=calibrantmz+plusminusvalues[calibrantnr]) |
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339 |
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340 ## in case m/z range includes only 1 m/z: |
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341 if (calibrantfeaturemin == calibrantfeaturemax){ |
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342 calibrantintensity = spectra(msidata)[calibrantfeaturemin,] |
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343 }else{ |
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344 ## if m/z range includes more than 1 m/z take sum of intensities |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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345 calibrantintensity = colSums(spectra(msidata)[calibrantfeaturemin:calibrantfeaturemax,]) |
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346 } |
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347 ## for each pixel add sum of intensity in the given m/z range |
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348 pixelmatrix = rbind(pixelmatrix, calibrantintensity) |
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349 } |
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350 |
2
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351 countvector= as.factor(colSums(pixelmatrix>0)) |
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352 countdf= cbind(coord(msidata)[,1:2], countvector) |
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353 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen") |
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354 |
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355 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+ |
3eee933c27cf
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356 geom_tile() + coord_fixed() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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357 ggtitle("Number of calibrants per pixel") + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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358 theme_bw() + |
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359 theme(plot.title = element_text(hjust = 0.5))+ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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360 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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361 scale_fill_manual(values = mycolours[1:length(countvector)], |
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362 na.value = "black", name = "# calibrants")) |
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363 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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364 ## append list for optional spectrum values output |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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365 colnames(countdf)[3] = "Number of Calibrants" |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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366 spectrum_list[[list_count]] = countdf |
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367 list_count = list_count+1 |
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368 |
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369 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")} |
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370 |
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371 ########################## 3) fold change image ########################### |
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372 |
1ccbda92b76b
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373 #if $calibrantratio: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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374 #for $foldchanges in $calibrantratio: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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375 mass1 = $foldchanges.mass1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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376 mass2 = $foldchanges.mass2 |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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377 distance = $foldchanges.distance |
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378 |
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379 ### if user did not write a label use input m/z as label |
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380 #if not str($foldchanges.filenameratioplot).strip(): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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381 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2) |
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382 #else: |
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383 #set $label = $foldchanges.filenameratioplot |
f6aa0cff777c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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384 #end if |
f6aa0cff777c
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385 |
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386 ### filter msidata for given m/z range (for both input m/z) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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387 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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388 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,] |
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389 |
9
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390 ### find m/z in the two given ranges with the highest mean intensity |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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391 ### this two m/z will be used to calculate the fold change (red line in plot) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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392 maxmassrow1 = rowMeans(spectra(filtered_data1)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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393 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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394 maxmassrow2 = rowMeans(spectra(filtered_data2)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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395 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)] |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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396 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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changeset
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397 ### plot legend: chosen value in blue, distance in blue, max m/z in red |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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changeset
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398 ### m/z range for each plot (fixed range of 5 Da) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
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399 ### xlim does not work because it does not adjust for the max. intensities within the range |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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400 mzdown1 = features(msidata, mz = mass1-2) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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401 mzup1 = features(msidata, mz = mass1+3) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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402 mzdown2 = features(msidata, mz = mass2-2) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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403 mzup2 = features(msidata, mz = mass2+3) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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404 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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405 ### plot for first m/z |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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406 par(mfrow=c(2,1), oma=c(0,0,2,0)) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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407 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da")) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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408 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3)) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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changeset
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409 abline(v=maxmass1, col="red", lty=5) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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410 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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411 ### plot for second m/z |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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412 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da")) |
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963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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413 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3)) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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414 abline(v=maxmass2, col="red", lty=5) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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415 title("Control of fold change plot", outer=TRUE) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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416 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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changeset
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417 ### filter spectra for max m/z to have two vectors, which can be divided |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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changeset
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418 ### plot spatial distribution of fold change |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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419 ### only possible when there are intensities > 0 in both given m/z ranges |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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420 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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421 if (length(maxmass1)>0&length(maxmass2)>0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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changeset
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422 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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423 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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424 foldchange= log2(mass1vector/mass2vector) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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changeset
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425 fcmatrix = cbind(foldchange, coord(msidata)[,1:2]) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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changeset
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426 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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427 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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428 geom_tile() + coord_fixed()+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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429 ggtitle("$label")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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430 theme_bw()+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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changeset
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431 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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changeset
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432 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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changeset
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433 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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434 ,space = "Lab", na.value = "black", name ="FC")) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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changeset
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435 }else{ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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436 plot(0,type='n',axes=FALSE,ann=FALSE) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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437 title(main=paste("At least one m/z range did not contain any intensity value > 0,\n therefore no foldchange plot could be drawn"))} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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438 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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439 #end for |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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440 #end if |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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441 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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442 #################### 4) m/z heatmaps ####################################### |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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443 |
3
f6aa0cff777c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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changeset
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444 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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445 if (length(inputmasses) != 0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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446 for (mass in 1:length(inputmasses)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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changeset
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447 image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton, |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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448 main= paste0(inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"), |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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changeset
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449 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy)) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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450 } |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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451 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")} |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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changeset
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452 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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453 #################### 5) Number of peaks per pixel - image ################## |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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454 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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changeset
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455 ## here every intensity value > 0 counts as pixel |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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456 peaksperpixel = colSums(spectra(msidata)[]> 0) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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changeset
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457 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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diff
changeset
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458 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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459 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff
changeset
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460 geom_tile() + coord_fixed() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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changeset
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461 ggtitle("Number of peaks per spectrum")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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changeset
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462 theme_bw() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
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463 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
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464 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
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465 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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changeset
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466 ,space = "Lab", na.value = "black", name = "# peaks")) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
467 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
468 ## append list for optional spectrum values output |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
469 colnames(peakscoordarray)[3] = "Number of Peaks" |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
470 spectrum_list[[list_count]] = peakscoordarray |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
471 list_count = list_count+1 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
472 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
473 ############################### 6) TIC image ############################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
474 |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
475 TICcoordarray=cbind(coord(msidata)[,1:2], TICs) |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
476 colo = colorRampPalette( |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
477 c("blue", "cyan", "green", "yellow","red")) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
478 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
479 geom_tile() + coord_fixed() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
480 ggtitle("Total Ion Chromatogram")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
481 theme_bw() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
482 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
483 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
484 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
485 ,space = "Lab", na.value = "black", name = "TIC")) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
486 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
487 ## append list for optional spectrum values output |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
488 colnames(TICcoordarray)[3] = "TIC per spectrum" |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
489 spectrum_list[[list_count]] = TICcoordarray |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
490 list_count = list_count+1 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
491 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
492 ############################### 7) Most abundant m/z image ################# |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
493 |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
494 highestmz = apply(spectra(msidata)[],2,which.max) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
495 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz]) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
496 colnames(highestmz_matrix)[3] = "highestmzinDa" |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
497 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
498 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
499 geom_tile() + coord_fixed() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
500 ggtitle("Most abundant m/z in each spectrum")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
501 theme_bw() + |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
502 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
503 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z", |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
504 labels = as.character(pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)]), |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
505 breaks = pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)], limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
506 theme(text=element_text(family="ArialMT", face="bold", size=12))) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
507 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
508 ## which m/z are highest |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
509 highestmz_peptides = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[1]) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
510 highestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == highestmz_peptides)[1] |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
511 |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
512 secondhighestmz = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[2]) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
513 secondhighestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == secondhighestmz)[1] |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
514 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
515 print(head(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE))) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
516 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
517 ## append list for optional spectrum values output |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
518 colnames(highestmz_matrix)[3] = "Most abundant m/z" |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
519 spectrum_list[[list_count]] = highestmz_matrix |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
520 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
521 ########################## 8) pca image for two components ################# |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
522 |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
523 pca = PCA(msidata, ncomp=2) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
524 par(mfrow = c(2,1)) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
525 plot(pca, col=c("black", "darkgrey"), main="PCA for two components") |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
526 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy)) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
527 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
528 ################## III) properties over spectra index ########## |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
529 ############################################################################## |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
530 print("properties over pixels") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
531 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
532 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
533 ########################## 9) number of peaks per spectrum ################# |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
534 ## 9a) scatterplot |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
535 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
536 title(xlab="Spectra index", line=3) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
537 title(ylab="Number of peaks", line=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
538 abline(v=abline_vector, lty = 3) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
539 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
540 ## 9b) histogram |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
541 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
542 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="") |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
543 title(main="Number of peaks per spectrum", line=2) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
544 title(ylab="Frequency = # spectra", line=4) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
545 abline(v=median(peaksperpixel), col="blue") |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
546 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
547 ## 9c) additional histogram to show subsample contributions |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
548 ## only when samples were combined before (combined_sample) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
549 if (!is.null(levels(msidata\$combined_sample))){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
550 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
551 df_9 = data.frame(peaksperpixel, msidata\$combined_sample) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
552 colnames(df_9) = c("Npeaks", "sample_name") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
553 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
554 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=sample_name)) + |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
555 geom_histogram()+ theme_bw()+ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
556 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
557 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
558 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
559 theme(legend.position="bottom",legend.direction="vertical")+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
560 labs(title="Number of peaks per spectrum and sample", x="Number of peaks per spectrum", y = "Frequency = # spectra") + |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
561 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
562 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
563 print(hist_9)} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
564 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
565 ########################## 10) TIC per spectrum ########################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
566 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
567 ## 10a)density scatterplot |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
568 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
569 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
570 title(xlab="Spectra index", line=3) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
571 title(ylab = "Total ion chromatogram intensity", line=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
572 abline(v=abline_vector, lty = 3) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
573 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
574 ## 10b) histogram |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
575 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="") |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
576 title(main= "TIC per spectrum", line=2) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
577 title(ylab="Frequency = # spectra", line=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
578 abline(v=median(log(TICs[TICs>0])), col="blue") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
579 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
580 ## 10c) additional histogram to show subsample contributions |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
581 ## only when samples were combined before (combined_sample) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
582 if (!is.null(levels(msidata\$combined_sample))){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
583 df_10 = data.frame(log(TICs), msidata\$combined_sample) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
584 colnames(df_10) = c("TICs", "sample_name") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
585 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
586 hist_10 = ggplot(df_10, aes(x=TICs, fill=sample_name)) + |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
587 geom_histogram()+ theme_bw()+ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
588 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
589 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
590 theme(legend.position="bottom",legend.direction="vertical")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
591 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
592 labs(title="TIC per spectrum and sample", x="log(TIC per spectrum)", y = "Frequency = # spectra") + |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
593 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
594 geom_vline(xintercept = median(log(TICs[TICs>0])), size = 1, colour = "black",linetype = "dashed") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
595 print(hist_10)} |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
596 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
597 ################################## IV) changes over m/z #################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
598 ############################################################################ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
599 print("changes over m/z") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
600 ########################## 11) Number of peaks per m/z ##################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
601 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
602 peakspermz = rowSums(spectra(msidata)[] > 0 ) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
603 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
604 par(mfrow = c(2,1), mar=c(5,6,4,4.5)) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
605 ## 11a) scatterplot |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
606 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
607 title(xlab="m/z", line=2.5) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
608 title(ylab = "Number of peaks", line=4) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
609 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
610 mtext("Coverage of spectra [%]", 4, line=3, adj=1) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
611 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
612 ## 11b) histogram |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
613 hist(peakspermz, main="", las=1, ylab="", xlab="") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
614 title(ylab = "Frequency", line=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
615 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
616 abline(v=median(peakspermz), col="blue") |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
617 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
618 ########################## 12) Sum of intensities per m/z ################## |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
619 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
620 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
621 mzTIC = rowSums(spectra(msidata)[]) ## calculate intensity sum for each m/z |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
622 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
623 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
624 ## 12a) scatterplot |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
625 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
626 title(xlab="m/z", line=2.5) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
627 title(ylab="Intensity sum", line=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
628 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
629 ## 12b) histogram |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
630 hist(log(mzTIC), main="", xlab = "", las=1, ylab="") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
631 title(main="Sum of intensities per m/z", line=2, ylab="") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
632 title(xlab = "log (sum of intensities per m/z)") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
633 title(ylab = "Frequency", line=4) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
634 abline(v=median(log(mzTIC[mzTIC>0])), col="blue") |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
635 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
636 ################################## V) general plots ######################## |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
637 ############################################################################ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
638 print("general plots") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
639 ########################## 13) Intensity distribution ###################### |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
640 |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
641 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
642 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
643 ## 13a) Median intensity over spectra |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
644 medianint_spectra = apply(spectra(msidata), 2, median) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
645 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
646 title(ylab="Median spectrum intensity", line=4) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
647 abline(v=abline_vector, lty = 3) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
648 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
649 ## 13b) histogram: |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
650 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
651 title(main="Log2-transformed intensities", line=2) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
652 title(xlab="log2 intensities") |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
653 title(ylab="Frequency", line=4) |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
654 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue") |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
655 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
656 ## 13c) histogram to show subsample contribution |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
657 ## only for previously combined samples |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
658 if (!is.null(levels(msidata\$combined_sample))){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
659 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
660 df_13 = data.frame(matrix(,ncol=2, nrow=0)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
661 for (subsample in levels(msidata\$combined_sample)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
662 log2_int_subsample = log2(spectra(msidata)[,msidata\$combined_sample==subsample]) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
663 df_subsample = data.frame(as.numeric(log2_int_subsample)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
664 df_subsample\$sample_name = subsample |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
665 df_13 = rbind(df_13, df_subsample)} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
666 df_13\$sample_name = as.factor(df_13\$sample_name) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
667 colnames(df_13) = c("logint", "sample_name") |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
668 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
669 hist_13 = ggplot(df_13, aes(x=logint, fill=sample_name)) + |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
670 geom_histogram()+ theme_bw()+ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
671 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
672 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") + |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
673 theme(plot.title = element_text(hjust = 0.5))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
674 theme(legend.position="bottom",legend.direction="vertical")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
675 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
676 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
677 geom_vline(xintercept = median(log2(spectra(msidata)[(spectra(msidata)>0)])), size = 1, colour = "black",linetype = "dashed") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
678 print(hist_13) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
679 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
680 ## 13d) boxplots to visualize in a different way the intensity distributions |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
681 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1)) |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
682 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
683 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
684 for (subsample in levels(msidata\$combined_sample)){ |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
|
685 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$combined_sample==subsample]) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
686 mean_matrix = cbind(mean_matrix, mean_mz_sample)} |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
687 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
|
688 boxplot(log2(mean_matrix), ylab = "log2 mean intensity per m/z", main="Mean intensities per m/z and sample", xaxt = "n") |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
|
689 (axis(1, at = c(1:number_combined), labels=levels(msidata\$combined_sample), cex.axis=cex_boxplot, las=2)) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
690 } |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
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diff
changeset
|
691 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
692 ########################## 14) Histogram on m/z values ##################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
693 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
694 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
695 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
696 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
697 ############################ 15) Mass spectra ############################## |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
698 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
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699 par(mfrow = c(2, 2)) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff
changeset
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700 pixels_for_plot = c(round(length(pixelnumber)/2, , digits=0), round(length(pixelnumber)/4, , digits=0), round(length(pixelnumber)/4*3, , digits=0)) |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
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701 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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changeset
|
702 plot(msidata, pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2]))) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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changeset
|
703 plot(msidata, pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2]))) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
704 plot(msidata, pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2]))) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
705 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
706 #################### 16) Zoomed in mass spectra for calibrants############## |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
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diff
changeset
|
707 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
708 count = 1 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
709 differencevector = numeric() |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
710 differencevector2 = vector() |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
711 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
712 if (length(inputcalibrantmasses) != 0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
713 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
714 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
715 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
716 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
717 for (mass in 1:length(inputcalibrantmasses)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
718 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
719 ### define the plot window with xmin und xmax |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
720 minmasspixel = features(msidata, mz=inputcalibrantmasses[mass]-1) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
721 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3) |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
722 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
723 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
724 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
725 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
726 maxmassrow = rowMeans(spectra(filtered_data)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
727 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highestaverage intensity in m/z range |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
728 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
729 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
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diff
changeset
|
730 }else{ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
731 ppmdifference = NA |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
732 maxvalue = NA} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
733 differencevector[mass] = round(ppmdifference, digits=2) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
734 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
735 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
736 mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### gives closest featurenumber which is closest to given m/z |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
737 mzvalue = mz(msidata)[mznumber] ### gives the closest m/z |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
738 mzdifference2 = mzvalue - inputcalibrantmasses[mass] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
739 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
740 differencevector2[mass] = round(ppmdifference2, digits=2) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
741 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
742 par(mfrow = c(2, 2), oma=c(0,0,2,0)) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
743 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum") |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
744 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,1,3)) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
745 abline(v=c(maxvalue), col="red", lty=2) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
746 abline(v=c(mzvalue), col="green2", lty=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
747 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2]))) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
|
748 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,1,3)) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
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diff
changeset
|
749 abline(v=c(maxvalue), col="red", lty=2) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
750 abline(v=c(mzvalue), col="green2", lty=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
751 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2]))) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
752 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,1,3)) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
753 abline(v=c(maxvalue), col="red", lty=2) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
754 abline(v=c(mzvalue), col="green2", lty=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
755 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2]))) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
756 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,1,3)) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
757 abline(v=c(maxvalue), col="red", lty=2) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
758 abline(v=c(mzvalue), col="green2", lty=4) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
759 title(paste0("theor. m/z: ", inputcalibrants[count,1]), col.main="blue", outer=TRUE, line=0, adj=0.074) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
760 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
761 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
762 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
763 ### 16b) one large extra plot with different colours for different samples (for combined_sample only) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
764 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
765 if (!is.null(levels(msidata\$combined_sample))){ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
766 if (number_combined < 10){ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
767 key_zoomed = TRUE |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
768 }else{key_zoomed = FALSE} |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
769 par(mfrow = c(1, 1)) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
770 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),main="average spectrum per sample", |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
771 pixel.groups=msidata\$combined_sample, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
772 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="black", lty=c(3,1,3)) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
773 count=count+1 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
774 } |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
775 } |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
776 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
777 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range######### |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
778 |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
779 par(mfrow = c(1, 1)) |
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
780 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
781 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value: |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
782 |
7
b86a66dd1a16
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents:
6
diff
changeset
|
783 calibrant_names = as.character(inputcalibrants[,2]) |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
784 diff_df = data.frame(differencevector, calibrant_names) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
785 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
786 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
787 print("plot 17: no peaks in the chosen region, repeat with higher ppm range") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
788 }else{ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
789 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
790 diff_plot=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
791 labs(title="Difference m/z with max. average intensity vs. theor. calibrant m/z", x="calibrants", y = "Difference in ppm")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
792 theme(plot.title = element_text(hjust = 0.5))+theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
793 geom_text(aes(label=differencevector), vjust=-0.3, size=3.5, col="blue") |
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
794 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
795 print(diff_plot)} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
796 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
797 ######### 18) ppm difference input calibrant m/z and closest m/z ########### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
798 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
799 ### plot the ppm difference calculated above theor. m/z value to closest m/z value: |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
800 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
801 differencevector2 = round(differencevector2, digits=2) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
802 calibrant_names = as.character(inputcalibrants[,2]) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
803 diff_df = data.frame(differencevector2, calibrant_names) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
804 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
805 diff_plot=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
806 labs(title="Difference closest measured m/z vs. theor. calibrant m/z", x="calibrants", y = "Difference in ppm")+ |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
807 theme(plot.title = element_text(hjust = 0.5))+theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
808 geom_text(aes(label=differencevector2), vjust=-0.3, size=3.5, col="blue") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
809 |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
810 print(diff_plot) |
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
811 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
812 #################### 19) ppm difference over pixels ##################### |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
813 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
814 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
815 count = 1 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
816 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata))) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
817 for (calibrant in inputcalibrantmasses){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
818 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, all ppm differences will be NA |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
819 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
820 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
821 if (nrow(filtered_data) > 0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
822 ### filtered for m/z range, now go through it pixel by pixel to find max peak in each spectrum |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
823 ppm_vector = numeric() |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
824 for (pixel_count in 1:ncol(filtered_data)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
825 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])] |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
826 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
827 mzdiff = mz_max - calibrant |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
828 ppmdiff = mzdiff/calibrant*1000000 |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
829 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
830 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
831 if (max(spectra(filtered_data)[,pixel_count]) == 0){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
832 ppmdiff = NA} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
833 ppm_vector[pixel_count] = ppmdiff} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
834 }else{ppm_vector = rep(NA, ncol(msidata))} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
835 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
836 ppm_df = cbind(ppm_df, ppm_vector) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
837 count=count+1} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
838 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
839 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
840 print("plot 19: no peaks in the chosen region, repeat with higher ppm range") |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
841 }else{ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
842 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
843 ### plot ppm differences over pixels (spectra index) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
844 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
845 par(mar=c(4.1, 4.1, 4.1, 7.5)) |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
846 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)") |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
847 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
848 for (each_cal in 1:ncol(ppm_df)){ |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
849 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
850 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
851 abline(v=abline_vector, lty = 3)} |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
852 |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
853 }else{print("16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")} |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
854 |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
855 dev.off() |
6
5c63fe03ed9e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents:
5
diff
changeset
|
856 |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
857 }else{ |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
858 print("inputfile has no intensities > 0") |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
859 dev.off() |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
860 } |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
861 |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
862 ## tabular output of spectra values |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
863 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
864 #if $pixel_output: |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
865 print("pixel list") |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
866 pixel_df = Reduce(function(...) merge(..., by=c("x", "y"), all=T), spectrum_list) |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
867 write.table(pixel_df, file="$pixel_tabular_output", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
868 #end if |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
869 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
870 |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
871 |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
872 ]]></configfile> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
873 </configfiles> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
874 <inputs> |
3
f6aa0cff777c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents:
2
diff
changeset
|
875 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
876 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
877 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
878 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
879 <option value="mz" >mz</option> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
880 <option value="ppm" selected="True" >ppm</option> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
881 </param> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
882 <param name="filename" type="text" value="" optional="true" label="Title" help="will appear as header in the quality report, if nothing given input dataset name is used"/> |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
883 <param name="calibrant_file" type="data" optional="true" format="tabular" |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
884 label="File with internal calibrants" help="first column: m/z, second column: name (optional), tabular file"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
885 <param name="peptide_file" type="data" optional="true" format="tabular" label="File with m/z of interest" |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
886 help="first column: m/z, second column: name (optional), tabular file"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
887 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range for m/z heatmaps (x-y grid)" help="Will be added in both directions to input calibrants and peptide m/z"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
888 <param name="plusminus_ppm" value="50" type="float" label="Ppm range for accuracy and number of calibrants plots" help="Will be added in both directions to input calibrant m/z"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
889 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10"> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
890 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
891 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
892 <param name="distance" value="0.25" type="float" label="M/z range" help="Plusminus m/z window added to input m/z. In both m/z ranges the maximum intensity is used to calculate the fold change"/> |
3
f6aa0cff777c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents:
2
diff
changeset
|
893 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
894 </repeat> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
895 <param name="pixel_output" type="boolean" display="radio" label="Tabular with spectra information" help="Values for each spectrum (pixel) in x-y grid images"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
896 </inputs> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
897 <outputs> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
898 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
899 <data format="tabular" name="pixel_tabular_output" label="$infile.display_name spectra information"> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
900 <filter>pixel_output</filter> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
901 </data> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
902 </outputs> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
903 <tests> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
904 <test expect_num_outputs="2"> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
905 <param name="infile" value="" ftype="imzml"> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
906 <composite_data value="Example_Processed.imzML"/> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
907 <composite_data value="Example_Processed.ibd"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
908 </param> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
909 <param name="accuracy" value="200"/> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
910 <param name="units" value="ppm"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
911 <param name="peptide_file" value="inputpeptides.txt"/> |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
912 <param name="calibrant_file" value="inputcalibrantfile1.txt"/> |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
913 <param name="plusminus_dalton" value="0.25"/> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
914 <param name="plusminus_ppm" value="100"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
915 <param name="filename" value="Testfile_imzml"/> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
916 <repeat name="calibrantratio"> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
917 <param name="mass1" value="328.9"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
918 <param name="mass2" value="398.8"/> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
919 <param name="distance" value="0.25"/> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
920 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
921 </repeat> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
922 <param name="pixel_output" value="True"/> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
923 <output name="pixel_tabular_output" file="spectra_info_imzml.txt"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
924 <output name="plots" file="QC_imzml.pdf" compare="sim_size" delta="20000"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
925 </test> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
926 <test expect_num_outputs="1"> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
927 <param name="infile" value="" ftype="analyze75"> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
928 <composite_data value="Analyze75.hdr"/> |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
929 <composite_data value="Analyze75.img"/> |
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
930 <composite_data value="Analyze75.t2m"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
931 </param> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
932 <param name="peptide_file" value="inputpeptides.txt"/> |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
933 <param name="calibrant_file" value="inputcalibrantfile2.txt"/> |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
934 <param name="plusminus_dalton" value="0.5"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
935 <param name="filename" value="Testfile_analyze75"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
936 <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
937 </test> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
938 <test expect_num_outputs="2"> |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
939 <param name="infile" value="123_combined.RData" ftype="rdata"/> |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
940 <param name="plusminus_dalton" value="0.2"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
941 <param name="filename" value="Testfile_rdata"/> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
942 <param name="pixel_output" value="True"/> |
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
943 <output name="pixel_tabular_output" file="spectra_info_123_combi.txt"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
944 <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/> |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
945 </test> |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
946 <test expect_num_outputs="1"> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
947 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
948 <param name="peptide_file" value="inputpeptides.txt"/> |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
949 <param name="calibrant_file" value="inputcalibrantfile2.txt"/> |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
950 <param name="plusminus_dalton" value="0.1"/> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
951 <param name="filename" value="Testfile_rdata"/> |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
952 <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/> |
2
1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents:
1
diff
changeset
|
953 </test> |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
954 </tests> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
955 <help> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
956 <![CDATA[ |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
957 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
958 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
959 This tool uses some Cardinal functions to create a quality control report with descriptive plots for mass spectrometry imaging data. |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
960 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
961 Input data: 3 types of input data can be used: |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
962 |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
963 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ |
0
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
964 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
965 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData) |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff
changeset
|
966 |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
967 Options: |
4
fef8bd551236
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents:
3
diff
changeset
|
968 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
969 - internal calibrants are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
970 - m/z of interest are used to generate m/z heatmaps (x-y grid) |
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
971 - optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio)) |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
972 |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
973 Output: |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
974 |
9
963c7ec00141
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents:
8
diff
changeset
|
975 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data |
10
3eee933c27cf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents:
9
diff
changeset
|
976 - optional spectra information as tabular file with numbers of calibrants (needs input calibrant file), numbers of peaks, TIC and most abundant m/z in each spectrum |
8
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
977 |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
|
978 Tip: |
52ef77866de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents:
7
diff
changeset
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979 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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980 - For additional m/z heatmaps use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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981 |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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982 ]]> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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983 </help> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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984 <citations> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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985 <citation type="doi">10.1093/bioinformatics/btv146</citation> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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986 </citations> |
845073d506a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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987 </tool> |
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1ccbda92b76b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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988 |