Mercurial > repos > galaxyp > msi_spectra_plot
changeset 4:dcf79af72c8f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
| author | galaxyp |
|---|---|
| date | Tue, 19 Jun 2018 18:06:46 -0400 |
| parents | 693a8efdfdeb |
| children | bc931322e4d6 |
| files | msi_spectra_plots.xml test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_empty_spectra.pdf test-data/Plot_imzml.pdf test-data/Plot_rdata.pdf |
| diffstat | 6 files changed, 124 insertions(+), 31 deletions(-) [+] |
line wrap: on
line diff
--- a/msi_spectra_plots.xml Mon Jun 11 17:33:12 2018 -0400 +++ b/msi_spectra_plots.xml Tue Jun 19 18:06:46 2018 -0400 @@ -1,10 +1,12 @@ -<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.1"> +<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.2"> <description> mass spectrometry imaging mass spectra plots </description> <requirements> <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> <requirement type="package" version="2.2.1">r-gridextra</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + <requirement type="package" version="0.5.0">r-scales</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -29,11 +31,11 @@ library(Cardinal) library(gridExtra) - -## Read MALDI Imaging dataset +library(ggplot2) +library(scales) #if $infile.ext == 'imzml' - msidata = readImzML('infile') + msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else @@ -71,9 +73,9 @@ ## Processing informations processinginfo = processingData(msidata) -centroidedinfo = processinginfo@centroided # TRUE or FALSE +centroidedinfo = processinginfo@centroided -## if TRUE write processinginfo if no write FALSE +## if TRUE write processinginfo if FALSE write FALSE ## normalization if (length(processinginfo@normalization) == 0) { @@ -101,7 +103,7 @@ } properties = c("Number of m/z features", - "Range of m/z values [Da]", + "Range of m/z values", "Number of pixels", "Range of x coordinates", "Range of y coordinates", @@ -208,35 +210,111 @@ ########################################################################### #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': - print("sample_pixel") + print("sample pixels") ##################### I) Sample: plot full mass spectrum ############## - plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=TRUE, col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) + ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot + if (!is.null(levels(msidata\$combined_sample))){ + print("combined samples") + + ## overview plot over combined sample, in case more than 10 combined_samples legend has to be taken from this plot + number_combined = length(levels(msidata\$combined_sample)) + + ## the more combined_samples a file has the smaller will be the legend + if (number_combined<20){ + legend_size = 10 + }else if (number_combined>20 && number_combined<40){ + legend_size = 9 + }else if (number_combined>40 && number_combined<60){ + legend_size = 8 + }else if (number_combined>60 && number_combined<100){ + legend_size = 7 + }else{ + legend_size = 6 + } + + position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample) + colnames(position_df)[3] = "sample_name" + + combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ + geom_tile() + + coord_fixed()+ + ggtitle("Spatial orientation of combined data")+ + theme_bw()+ + theme(plot.title = element_text(hjust = 0.5))+ + theme(text=element_text(family="ArialMT", face="bold", size=12))+ + theme(legend.position="bottom",legend.direction="vertical")+ + theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+ + guides(fill=guide_legend(ncol=5,byrow=TRUE)) + coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) + coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) + for(file_count in 1:nrow(coord_labels)) + {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], + y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} + + print(combine_plot) + + ## print legend only for less than 10 samples + if (length(levels(msidata\$combined_sample)) < 10){ + key_legend = TRUE + }else{key_legend = FALSE} + + plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE) + }else{ + plot(msidata, pixel=1:ncol(msidata), key=TRUE)} ##################### II) Sample: plot zoom-in mass spectrum ########## #if $pixel_conditional.zoomed_sample: #for $token in $pixel_conditional.zoomed_sample: + print("zoomed sample pixels") minmasspixel = features(msidata, mz=$token.xlimmin) maxmasspixel = features(msidata, mz=$token.xlimmax) - plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), - xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample, - key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE) + ## coloured plot with mean over all spectra for combined_sample, otherwise only 1 black plot + if (!is.null(levels(msidata\$combined_sample))){ + print("combined samples") + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), + xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$combined_sample, + key=key_legend,col=hue_pal()(length(levels(msidata\$combined_sample))), superpose=TRUE) + }else{ + plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))} #end for #end if - - pixeldf = data.frame(table(msidata\$combined_sample)) + if (!is.null(levels(msidata\$combined_sample))){ + pixeldf = data.frame(table(msidata\$combined_sample)) + }else{ + pixeldf = data.frame("$filename", ncol(msidata))} colnames(pixeldf) = c("sample name", "number of pixels") #end if + ### overview table of pixels or samples: plot(0,type='n',axes=FALSE,ann=FALSE) title(main="Overview of chosen pixel:") - grid.table(pixeldf, rows= NULL) + + ### for more than 20 combined samples print only 20 samples per page: + if (is.null(levels(msidata\$combined_sample))){ + grid.table(pixeldf, rows= NULL) + }else if (length(levels(msidata\$combined_sample)) <= 20){ + grid.table(pixeldf, rows= NULL) + }else{ + grid.table(pixeldf[1:20,], rows= NULL) + mincount = 21 + maxcount = 40 + for (count20 in 1:(ceiling(nrow(pixeldf)/20)-1)){ + plot(0,type='n',axes=FALSE,ann=FALSE) + if (maxcount <= nrow(pixeldf)){ + grid.table(pixeldf[mincount:maxcount,], rows= NULL) + mincount = mincount+20 + maxcount = maxcount+20 + }else{### stop last page with last sample otherwise NA in table + grid.table(pixeldf[mincount:nrow(pixeldf),], rows= NULL)} + } + } dev.off() @@ -249,6 +327,11 @@ <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="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"/> + <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> + <option value="mz" >mz</option> + <option value="ppm" selected="True" >ppm</option> + </param> <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"> @@ -353,10 +436,25 @@ <param name="inputx" value="2"/> <param name="inputy" value="2"/> </repeat> - </conditional> + </conditional> <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/> </test> <test> + <param name="infile" value="" ftype="analyze75"> + <composite_data value="Analyze75.hdr"/> + <composite_data value="Analyze75.img"/> + <composite_data value="Analyze75.t2m"/> + </param> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="sample_pixel"/> + <repeat name="zoomed_sample"> + <param name="xlimmin" value="1250"/> + <param name="xlimmax" value="1270"/> + </repeat> + </conditional> + <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size" delta="20000"/> + </test> + <test> <param name="infile" value="123_combined.RData" ftype="rdata"/> <conditional name="pixel_conditional"> <param name="pixel_type" value="sample_pixel"/> @@ -364,23 +462,19 @@ <param name="xlimmin" value="350"/> <param name="xlimmax" value="360"/> </repeat> - </conditional> + </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"/> - <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="1000"/> - <param name="xlimmax" value="1050"/> - </repeat> - </repeat> + <conditional name="pixel_conditional"> + <param name="pixel_type" value="single_pixel"/> + <repeat name="repeatpixel"> + <param name="plusminusinDalton" value="0.1"/> + <param name="inputx" value="1"/> + <param name="inputy" value="1"/> + </repeat> + </conditional> <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/> </test> </tests> @@ -403,9 +497,8 @@ - Enter the x and y coordinates of your pixel of interest - 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 +- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for the sample/each combined sample - - 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 m/z value to define the limits of the plot Output: