msi_spectra_plot: msi_spectra_plots.xml comparison

comparison msi_spectra_plots.xml @ 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

comparison

equal deleted inserted replaced

-:ea4f1c516368
+:fe28ca73548a
-<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>
 <requirements>
 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
 Rscript '${MSI_mzplots}'
 ]]>
 </command>
 <configfiles>
 <configfile name="MSI_mzplots"><![CDATA[
 ################################# load libraries and read file #################
 library(Cardinal)
 library(gridExtra)
 load('infile.RData')
 #end if
 ###################################### 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)
 pixelcount = length(pixels(msidata))
 ## Range x coordinates
 minint = round(min(spectra(msidata)[]), digits=2)
 maxint = round(max(spectra(msidata)[]), digits=2)
 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)
 ## Number of empty TICs
 TICs = colSums(spectra(msidata)[])
 peakpickinginfo='FALSE'
 } else {
 peakpickinginfo=processinginfo@peakPicking
 }
-properties = c("Number of mz features",
+properties = c("Number of m/z features",
-"Range of mz values [Da]",
+"Range of m/z values [Da]",
 "Number of pixels",
 "Range of x coordinates",
 "Range of y coordinates",
 "Range of intensities",
 "Median of intensities",
 paste0(peakpickinginfo),
 paste0(centroidedinfo))
 property_df = data.frame(properties, values)
-print("before pdf")
 ######################################## PDF ###################################
 ################################################################################
 ################################################################################
 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
 plot(0,type='n',axes=FALSE,ann=FALSE)
+#if not $filename:
-title(main=paste0("Plotted mass spectra for file: \n\n", "$infile.display_name"))
+#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")
 #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=", $chosenpixel.inputy)
-print(pixelname)
-print(colnames(pixeldf))
-print(colnames(cbind(pixelname, pixelisvalid)))
 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
-print(colnames(pixeldf))
 ############################# II) control image ####################
-####################################################################
+if (pixelisvalid == "TRUE"){
+print(pixelisvalid)
-if (pixelisvalid == "TRUE")
-{
+image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
+colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram",
-print(pixelisvalid)
+main= paste0("x= ",$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 $chosenpixel.zoomedplot:
 minmasspixel = features(msidata, mz=$token.xlimmin)
 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
 xlim= c($token.xlimmin,$token.xlimmax))
 #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")
+############################# sample pixel ################################
+###########################################################################
 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
 print("sample_pixel")
-##################### I) Sample: plot full mass spectrum ###########
+##################### 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)
+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 #######
+##################### 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
 plot(0,type='n',axes=FALSE,ann=FALSE)
 title(main="Overview of chosen pixel:")
 grid.table(pixeldf, rows= NULL)
 dev.off()
 }else{
 print("Inputfile has no intensities > 0")
 dev.off()
 }
 ]]></configfile>
 </configfiles>
 <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>
 <option value="sample_pixel">All pixels of a sample</option>
 </param>
 <when value="single_pixel">
 <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="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="mass range for this mz value" help="plusminus mass window in Dalton"/>
+<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>
 <option value="grey">grey</option>
 <option value="blue">blue</option>
 <option value="dashed">dashed</option>
 <option value="dotted">dotted</option>
 <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">
+<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 mz for zoomed in window"/>
+<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 mz 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">
+<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 mz for zoomed in window"/>
+<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 mz 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>
 <param name="infile" value="" ftype="imzml">
 <composite_data value="Example_Continuous.imzML"/>
 <repeat name="repeatpixel">
 <param name="plusminusinDalton" value="0.25"/>
 <param name="inputx" value="3"/>
 <param name="inputy" value="3"/>
 <repeat name="zoomedplot">
-<param name="xlimmin" value="550"/>
+<param name="xlimmin" value="310"/>
-<param name="xlimmax" value="555"/>
+<param name="xlimmax" value="320"/>
 </repeat>
 <repeat name="zoomedplot">
-<param name="xlimmin" value="750"/>
+<param name="xlimmin" value="350"/>
-<param name="xlimmax" value="800"/>
+<param name="xlimmax" value="400"/>
 </repeat>
 <repeat name="zoomedplot">
 <param name="xlimmin" value="400"/>
 <param name="xlimmax" value="420"/>
 </repeat>
 </repeat>
 </conditional>
 <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">
 <param name="xlimmin" value="350"/>
 <param name="xlimmax" value="360"/>
 </tests>
 <help><![CDATA[
 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:
 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
 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.
+- 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 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
-- "All pixels of a sample": Returns a full average mass-spectrum plot with different colours for each subfile
+- "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"
 ]]>
 </help>
 <citations>

Mercurial > repos > galaxyp > msi_spectra_plot

comparison msi_spectra_plots.xml @ 3:fe28ca73548a draft