Mercurial > repos > galaxyp > msi_spectra_plot
diff msi_spectra_plots.xml @ 2:ea4f1c516368 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
| author | galaxyp |
|---|---|
| date | Mon, 28 May 2018 12:39:59 -0400 |
| parents | 7caaf84a8a51 |
| children | fe28ca73548a |
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--- a/msi_spectra_plots.xml Mon Apr 23 17:20:15 2018 -0400 +++ b/msi_spectra_plots.xml Mon May 28 12:39:59 2018 -0400 @@ -1,21 +1,20 @@ -<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.7.0.1"> +<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.0"> <description> mass spectrometry imaging mass spectra plots </description> <requirements> - <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement> + <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> <requirement type="package" version="2.2.1">r-gridextra</requirement> - <requirement type="package" version="2.23-15">r-kernsmooth</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ #if $infile.ext == 'imzml' - cp '${infile.extra_files_path}/imzml' infile.imzML && - cp '${infile.extra_files_path}/ibd' infile.ibd && + ln -s '${infile.extra_files_path}/imzml' infile.imzML && + ln -s '${infile.extra_files_path}/ibd' infile.ibd && #elif $infile.ext == 'analyze75' - cp '${infile.extra_files_path}/hdr' infile.hdr && - cp '${infile.extra_files_path}/img' infile.img && - cp '${infile.extra_files_path}/t2m' infile.t2m && + ln -s '${infile.extra_files_path}/hdr' infile.hdr && + ln -s '${infile.extra_files_path}/img' infile.img && + ln -s '${infile.extra_files_path}/t2m' infile.t2m && #else ln -s $infile infile.RData && #end if @@ -25,23 +24,22 @@ </command> <configfiles> <configfile name="MSI_mzplots"><![CDATA[ -################################# load libraries and read file ######################### +################################# load libraries and read file ################# library(Cardinal) library(gridExtra) -library(KernSmooth) ## Read MALDI Imaging dataset #if $infile.ext == 'imzml' - msidata <- readMSIData('infile.imzML') + msidata = readImzML('infile') #elif $infile.ext == 'analyze75' - msidata <- readMSIData('infile.hdr') + msidata = readAnalyze('infile') #else load('infile.RData') #end if -###################################### file properties in numbers ###################### +###################################### file properties in numbers ############## ## Number of features (mz) maxfeatures = length(features(msidata)) @@ -135,10 +133,11 @@ property_df = data.frame(properties, values) +print("before pdf") -######################################## PDF ############################################# -########################################################################################## -########################################################################################## +######################################## PDF ################################### +################################################################################ +################################################################################ pdf("mzplots.pdf", fonts = "Times", pointsize = 12) @@ -147,88 +146,108 @@ title(main=paste0("Plotted mass spectra for file: \n\n", "$infile.display_name")) -############################# I) numbers #################################### -############################################################################# +############################# I) numbers ###################################### +############################################################################### + +print("in pdf") grid.table(property_df, rows= NULL) -counting = 2 - outputmatrix = matrix(mz(msidata), ncol=1, byrow=TRUE) - colnames(outputmatrix) = "m/z" if (npeaks > 0) { pixeldf = data.frame(matrix(ncol = 2, nrow=0)) - #for $chosenpixel in $repeatpixel: + + #if str( $pixel_conditional.pixel_type) == 'single_pixel': + print("single_pixel") + + #for $chosenpixel in $pixel_conditional.repeatpixel: - ### is x and y which was put in to define pixel valid coordinates? - pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y) - pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy) - pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) + pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y) + pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy) + print(pixelname) + print(colnames(pixeldf)) + print(colnames(cbind(pixelname, pixelisvalid))) + pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) + print(colnames(pixeldf)) + + ############################# II) control image #################### + #################################################################### -############################# II) control image ############################# -############################################################################# + if (pixelisvalid == "TRUE") + { + + print(pixelisvalid) - if (pixelisvalid == "TRUE") - { + image(msidata, mz=$chosenpixel.inputmz, + ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram", + main= paste0("x= ",$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=$chosenpixel.inputwidth) - image(msidata, mz=$chosenpixel.inputmz, - ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram", - main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy)) + ##################### III) plot full mass spectrum ################# + #################################################################### + + plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) + + ##################### IV) plot zoom-in mass spectrum ############### + #################################################################### - abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) - abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) + #if $chosenpixel.zoomedplot: + #for $token in $chosenpixel.zoomedplot: + minmasspixel = features(msidata, mz=$token.xlimmin) + maxmasspixel = features(msidata, mz=$token.xlimmax) + + plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), + xlim= c($token.xlimmin,$token.xlimmax)) - ##################### III) plot full mass spectrum ########################## - ############################################################################# + #end for + #end if - plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) + }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") - ##################### IV) plot zoom-in 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) - #if $chosenpixel.zoomedplot: - #for $token in $chosenpixel.zoomedplot: + ##################### 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=$token.xlimmax) - - plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), - xlim= c($token.xlimmin,$token.xlimmax)) + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=pData(msidata)\$sample, key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) #end for #end if - ##################### V) Output with mz and intensities ##################### - ############################################################################# - - - ### for each repeat a new intensity column for the new pixel is added - outputmatrix = cbind(outputmatrix, spectra(msidata)[,pixels(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))]) - colnames(outputmatrix)[counting] = paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy, " intensity") - counting = counting+1 + pixeldf = data.frame(table(pData(msidata)\$sample)) + colnames(pixeldf) = c("sample name", "number of pixels") - }else{ - print("These pixel coordinates did not correspond to a real pixel")} + #end if -#end for - - colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file") plot(0,type='n',axes=FALSE,ann=FALSE) - title(main=paste0("Overview of chosen pixel for file:\n", "$infile.display_name")) + title(main="Overview of chosen pixel:") grid.table(pixeldf, rows= NULL) dev.off() - write.table(outputmatrix, file="$tabularmatrix", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t") + }else{ print("Inputfile has no intensities > 0") dev.off() @@ -238,35 +257,48 @@ <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)"/> - <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="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="red">red</option> - <option value="green">green</option> + <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> - <param name="inputtype" type="select" label="select the line type for the lines at x and y position"> - <option value="solid" selected="True">solid</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"> - <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> - </repeat> + <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="plusminusinDalton" value="0.25" type="float" label="mass range for this mz value" help="plusminus mass 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="red">red</option> + <option value="green">green</option> + </param> + <param name="inputtype" type="select" label="select the line type for the lines at x and y position"> + <option value="solid" selected="True">solid</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"> + <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> + </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> + </when> + </conditional> </inputs> <outputs> <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "${tool.name} ${on_string}"/> - <data format="tabular" name="tabularmatrix" label="Mass spectrum ${on_string}" /> </outputs> <tests> <test> @@ -274,77 +306,76 @@ <composite_data value="Example_Continuous.imzML"/> <composite_data value="Example_Continuous.ibd"/> </param> - <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="xlimmax" value="555"/> - </repeat> - <repeat name="zoomedplot"> - <param name="xlimmin" value="750"/> - <param name="xlimmax" value="800"/> - </repeat> - <repeat name="zoomedplot"> - <param name="xlimmin" value="400"/> - <param name="xlimmax" value="420"/> - </repeat> - </repeat> - <repeat name="repeatpixel"> - <param name="plusminusinDalton" value="0.25"/> - <param name="inputx" value="2"/> - <param name="inputy" value="2"/> - </repeat> - <repeat name="repeatpixel"> - <param name="plusminusinDalton" value="0.25"/> - <param name="inputx" value="1"/> - <param name="inputy" value="1"/> - </repeat> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="single_pixel"/> + <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="xlimmax" value="555"/> + </repeat> + <repeat name="zoomedplot"> + <param name="xlimmin" value="750"/> + <param name="xlimmax" value="800"/> + </repeat> + <repeat name="zoomedplot"> + <param name="xlimmin" value="400"/> + <param name="xlimmax" value="420"/> + </repeat> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="2"/> + <param name="inputy" value="2"/> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="1"/> + <param name="inputy" value="1"/> + </repeat> + </conditional> <output name="plots" file="Plot_imzml.pdf" compare="sim_size" delta="20000"/> - <output name="tabularmatrix" file="Matrix_imzml.txt"/> </test> - <test> <param name="infile" value="" ftype="analyze75"> <composite_data value="Analyze75.hdr"/> <composite_data value="Analyze75.img"/> <composite_data value="Analyze75.t2m"/> </param> - <repeat name="repeatpixel"> - <param name="plusminusinDalton" value="0.25"/> - <param name="inputx" value="5"/> - <param name="inputy" value="2"/> - <repeat name="zoomedplot"> - <param name="xlimmin" value="840"/> - <param name="xlimmax" value="850"/> - </repeat> - </repeat> - <repeat name="repeatpixel"> - <param name="plusminusinDalton" value="0.25"/> - <param name="inputx" value="2"/> - <param name="inputy" value="2"/> - </repeat> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="single_pixel"/> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="5"/> + <param name="inputy" value="2"/> + <repeat name="zoomedplot"> + <param name="xlimmin" value="840"/> + <param name="xlimmax" value="850"/> + </repeat> + </repeat> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.25"/> + <param name="inputx" value="2"/> + <param name="inputy" value="2"/> + </repeat> + </conditional> <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/> - <output name="tabularmatrix" file="Matrix_analyze75.txt"/> - </test> - - <test> - <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> - <repeat name="repeatpixel"> - <param name="plusminusinDalton" value="0.25"/> - <param name="inputx" value="2"/> - <param name="inputy" value="2"/> - <repeat name="zoomedplot"> - <param name="xlimmin" value="222"/> - <param name="xlimmax" value="244"/> - </repeat> - </repeat> - <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/> - <output name="tabularmatrix" file="Matrix_rdata.txt"/> </test> <test> - <param name="infile" value="LM8_file16.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"/> + </repeat> + </conditional> + <output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/> + </test> + <test> + <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> <param name="plusminusinDalton" value="0.1"/> <param name="inputx" value="1"/> <param name="inputy" value="1"/> @@ -357,23 +388,41 @@ <param name="xlimmax" value="1050"/> </repeat> </repeat> - <output name="plots" file="Plot_LM8_file16.pdf" compare="sim_size" delta="20000"/> - <output name="tabularmatrix" file="Matrix_LM8.txt"/> + <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/> </test> </tests> <help><![CDATA[ -Returns a full mass-spectrum plot and peaklist output with masses and intensities for the chosen pixel. Input needs the x and the y coordinates of the pixel of interest. -Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mz value to define the limits of the plot. -To have a visual control that the right pixel was chosen, a heatmap of a mass in Dalton which can be specified will be plotted and two intersecting lines will show where the chosen pixel is located in the ion image. +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. 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 <http://ms-imaging.org/wp/introduction/>`_ +- 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) -The output of this tool contains a heatmap of the mass of interest with two lines intersecting at the pixel of interest. Then the full mass-spectrum plot is obtained and if chosen also several zoomed in mass spectra. A peaklist with masses and intensities for this pixel is exported as tabular file. +Options: + +- "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 + + - 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 + +Output: + +- 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" + ]]> </help>