Mercurial > repos > galaxyp > msi_spectra_plot
changeset 3:fe28ca73548a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit a7be47698f53eb4f00961192327d93e8989276a7
| author | galaxyp |
|---|---|
| date | Mon, 11 Jun 2018 17:34:44 -0400 |
| parents | ea4f1c516368 |
| children | 9eef2792afa4 |
| files | msi_spectra_plots.xml test-data/123_combined.RData test-data/123_combined.rdata test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/Plot_analyze75.pdf test-data/Plot_empty_spectra.pdf test-data/Plot_imzml.pdf test-data/Plot_rdata.pdf |
| diffstat | 9 files changed, 371 insertions(+), 438 deletions(-) [+] |
line wrap: on
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--- a/msi_spectra_plots.xml Mon May 28 12:39:59 2018 -0400 +++ b/msi_spectra_plots.xml Mon Jun 11 17:34:44 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.0"> +<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.1"> <description> mass spectrometry imaging mass spectra plots </description> @@ -24,6 +24,7 @@ </command> <configfiles> <configfile name="MSI_mzplots"><![CDATA[ + ################################# load libraries and read file ################# library(Cardinal) @@ -41,9 +42,9 @@ ###################################### file properties in numbers ############## -## Number of features (mz) +## Number of features (m/z) maxfeatures = length(features(msidata)) -## Range mz +## Range m/z minmz = round(min(mz(msidata)), digits=2) maxmz = round(max(mz(msidata)), digits=2) ## Number of spectra (pixels) @@ -60,7 +61,7 @@ medint = round(median(spectra(msidata)[]), digits=2) ## Number of intensities > 0 npeaks= sum(spectra(msidata)[]>0) -## Spectra multiplied with mz (potential number of peaks) +## Spectra multiplied with m/z (potential number of peaks) numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) ## Percentage of intensities > 0 percpeaks = round(npeaks/numpeaks*100, digits=2) @@ -99,8 +100,8 @@ peakpickinginfo=processinginfo@peakPicking } -properties = c("Number of mz features", - "Range of mz values [Da]", +properties = c("Number of m/z features", + "Range of m/z values [Da]", "Number of pixels", "Range of x coordinates", "Range of y coordinates", @@ -133,8 +134,6 @@ property_df = data.frame(properties, values) -print("before pdf") - ######################################## PDF ################################### ################################################################################ ################################################################################ @@ -142,62 +141,50 @@ pdf("mzplots.pdf", fonts = "Times", pointsize = 12) plot(0,type='n',axes=FALSE,ann=FALSE) - -title(main=paste0("Plotted mass spectra for file: \n\n", "$infile.display_name")) +#if not $filename: + #set $filename = $infile.display_name +#end if +title(main=paste0("Plotted mass spectra for file: \n\n","$filename")) ############################# I) numbers ###################################### ############################################################################### -print("in pdf") grid.table(property_df, rows= NULL) - +if (npeaks > 0){ -if (npeaks > 0) -{ pixeldf = data.frame(matrix(ncol = 2, nrow=0)) + ############################# single pixel ################################ + ########################################################################### #if str( $pixel_conditional.pixel_type) == 'single_pixel': - print("single_pixel") + print("single_pixel") #for $chosenpixel in $pixel_conditional.repeatpixel: - pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y) pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy) - print(pixelname) - print(colnames(pixeldf)) - print(colnames(cbind(pixelname, pixelisvalid))) pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) - print(colnames(pixeldf)) ############################# II) control image #################### - #################################################################### - - if (pixelisvalid == "TRUE") - { + if (pixelisvalid == "TRUE"){ + print(pixelisvalid) - print(pixelisvalid) - - - image(msidata, mz=$chosenpixel.inputmz, - ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram", - main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy)) + image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1), + colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram", + main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy)) abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) - ##################### III) plot full mass spectrum ################# - #################################################################### plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) ##################### IV) plot zoom-in mass spectrum ############### - #################################################################### #if $chosenpixel.zoomedplot: #for $token in $chosenpixel.zoomedplot: @@ -210,33 +197,39 @@ #end for #end if - }else{ print("The pixel coordinates did not correspond to a real pixel")} - #end for colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file") - #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': - print("sample_pixel") + + ############################# sample pixel ################################ + ########################################################################### - ##################### I) Sample: plot full mass spectrum ########### - plot(msidata, pixel=1:ncol(msidata), pixel.groups=pData(msidata)\$sample, key=TRUE, col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) + #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': + print("sample_pixel") - ##################### II) Sample: plot zoom-in mass spectrum ####### + ##################### I) Sample: plot full mass spectrum ############## + + plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=TRUE, col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) + + ##################### II) Sample: plot zoom-in mass spectrum ########## #if $pixel_conditional.zoomed_sample: #for $token in $pixel_conditional.zoomed_sample: minmasspixel = features(msidata, mz=$token.xlimmin) maxmasspixel = features(msidata, mz=$token.xlimmax) - plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=pData(msidata)\$sample, key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) + + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), + xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample, + key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) #end for #end if - pixeldf = data.frame(table(pData(msidata)\$sample)) + pixeldf = data.frame(table(msidata\$combined_sample)) colnames(pixeldf) = c("sample name", "number of pixels") #end if @@ -247,7 +240,6 @@ dev.off() - }else{ print("Inputfile has no intensities > 0") dev.off() @@ -257,6 +249,7 @@ <inputs> <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> + <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> <conditional name="pixel_conditional"> <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or of all pixels of a sample"> <option value="single_pixel" selected="True">Single pixel</option> @@ -266,8 +259,8 @@ <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20"> <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/> <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/> - <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here mz in Dalton" help="mz will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/> - <param name="plusminusinDalton" value="0.25" type="float" label="mass range for this mz value" help="plusminus mass window in Dalton"/> + <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here m/z in Dalton" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/> + <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window in Dalton"/> <param name="inputcolour" type="select" label="select the colour for the lines at x and y position"> <option value="white" selected="True">white</option> <option value="black">black</option> @@ -283,22 +276,22 @@ <option value="longdash">longdash</option> </param> <param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/> - <repeat name="zoomedplot" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50"> - <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/> - <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/> + <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50"> + <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum m/z for zoomed in window"/> </repeat> </repeat> </when> <when value="sample_pixel"> - <repeat name="zoomed_sample" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50"> - <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/> - <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/> + <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50"> + <param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum m/z for zoomed in window"/> </repeat> </when> </conditional> </inputs> <outputs> - <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "${tool.name} ${on_string}"/> + <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "$infile.display_name mass_spectra"/> </outputs> <tests> <test> @@ -313,12 +306,12 @@ <param name="inputx" value="3"/> <param name="inputy" value="3"/> <repeat name="zoomedplot"> - <param name="xlimmin" value="550"/> - <param name="xlimmax" value="555"/> + <param name="xlimmin" value="310"/> + <param name="xlimmax" value="320"/> </repeat> <repeat name="zoomedplot"> - <param name="xlimmin" value="750"/> - <param name="xlimmax" value="800"/> + <param name="xlimmin" value="350"/> + <param name="xlimmax" value="400"/> </repeat> <repeat name="zoomedplot"> <param name="xlimmin" value="400"/> @@ -364,7 +357,7 @@ <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/> </test> <test> - <param name="infile" value="123_combined.rdata" ftype="rdata"/> + <param name="infile" value="123_combined.RData" ftype="rdata"/> <conditional name="pixel_conditional"> <param name="pixel_type" value="sample_pixel"/> <repeat name="zoomed_sample"> @@ -395,7 +388,7 @@ Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_ -This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass-spectrometry imaging data. +This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data. Input data: 3 types of input data can be used: @@ -405,23 +398,23 @@ Options: -- "single pixel": Returns a full mass-spectrum plot for one pixel, which is defined by its x- and y-coordinates +- "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates - Enter the x and y coordinates of your pixel of interest - - To have a visual control for the selected pixel, a heatmap of a mass of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an mass of interest together with a mass range and for the lines the colour and type. - - Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mass value to define the limits of the plot -- "All pixels of a sample": Returns a full average mass-spectrum plot with different colours for each subfile + - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type. + - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot +- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each subfile - This option only works on files that have previosly been combined in the combine tool - - Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mass value to define the limits of the plot + - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot Output: -- Pdf with the selected mass-spectra plots and additional control plots +- Pdf with the selected mass spectra plots and additional control plots Tip: -- Corresponding peaklists with masses and their intensities can be obtained with the filtering tool option "ranges for x and y" +- Corresponding mass spectra with m/z intensity pairs as tabular output can be obtained with the filtering tool option "ranges for x and y" ]]>
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