Mercurial > repos > galaxyp > msi_spectra_plot
changeset 6:2e0368a6bfe8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 5bceedc3a11c950790692a4c64bbb83d46897bee
| author | galaxyp |
|---|---|
| date | Tue, 24 Jul 2018 04:53:42 -0400 |
| parents | 4f13aec6d8ff |
| children | 7d94faee0731 |
| 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 test-data/annotations.tabular |
| diffstat | 7 files changed, 88 insertions(+), 42 deletions(-) [+] |
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--- a/msi_spectra_plots.xml Fri Jul 06 14:14:41 2018 -0400 +++ b/msi_spectra_plots.xml Tue Jul 24 04:53:42 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.3"> +<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.4"> <description> mass spectrometry imaging mass spectra plots </description> @@ -152,7 +152,7 @@ #if not $filename: #set $filename = $infile.display_name #end if -title(main=paste0("Plotted mass spectra for file: \n\n","$filename")) +title(main=paste0("Mass spectra for file: \n\n","$filename")) ############################# I) numbers ###################################### @@ -219,16 +219,36 @@ #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': print("sample pixels") + ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample) + + #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation': + + ## read and extract x,y,annotation information + input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE) + annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)] + colnames(annotation_input) = c("x", "y", "annotation") + + ## merge with coordinate information of msidata + msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata))) + colnames(msidata_coordinates)[3] = "pixel_index" + merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE) + merged_annotation[is.na(merged_annotation)] = "NA" + merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),] + msidata\$annotation = as.factor(merged_annotation[,4]) + + #end if + ##################### I) Sample: plot full mass spectrum ############## - ## 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") + ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample + + if (!is.null(levels(msidata\$annotation))){ + print("annotated 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)) + ## overview plot over annotated samples + number_combined = length(levels(msidata\$annotation)) - ## the more combined_samples a file has the smaller will be the legend + ## the more annotation groups a file has the smaller will be the legend if (number_combined<20){ legend_size = 10 }else if (number_combined>20 && number_combined<40){ @@ -241,37 +261,31 @@ legend_size = 6 } - position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample) + position_df = cbind(coord(msidata)[,1:2], msidata\$annotation) 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")+ + ggtitle("Spatial orientation of annotated 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){ + if (length(levels(msidata\$annotation)) < 10){ key_legend = TRUE }else{key_legend = FALSE} - spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero - - plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE) + is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero + plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE) }else{ - spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero + is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero plot(msidata, pixel=1:ncol(msidata), key=TRUE)} ##################### II) Sample: plot zoom-in mass spectrum ########## @@ -284,20 +298,20 @@ minmasspixel = features(msidata, mz=$token.xlimmin) maxmasspixel = features(msidata, mz=$token.xlimmax) - ## 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") + ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot + if (!is.null(levels(msidata\$annotation))){ + print("annotation 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) + xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, + key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE) }else{ plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))} #end for #end if - if (!is.null(levels(msidata\$combined_sample))){ - pixeldf = data.frame(table(msidata\$combined_sample)) + if (!is.null(levels(msidata\$annotation))){ + pixeldf = data.frame(table(msidata\$annotation)) }else{ pixeldf = data.frame("$filename", ncol(msidata))} colnames(pixeldf) = c("sample name", "number of pixels") @@ -313,10 +327,10 @@ plot(0,type='n',axes=FALSE,ann=FALSE) title(main="Overview of chosen pixel:") - ### for more than 20 combined samples print only 20 samples per page: - if (is.null(levels(msidata\$combined_sample))){ + ### for more than 20 annotation groups print only 20 samples per page: + if (is.null(levels(msidata\$annotation))){ grid.table(pixeldf, rows= NULL) - }else if (length(levels(msidata\$combined_sample)) <= 20){ + }else if (length(levels(msidata\$annotation)) <= 20){ grid.table(pixeldf, rows= NULL) }else{ grid.table(pixeldf[1:20,], rows= NULL) @@ -368,8 +382,8 @@ <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 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="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" 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 "/> <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> @@ -386,15 +400,30 @@ </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 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"/> + <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/> </repeat> </repeat> </when> <when value="sample_pixel"> + <conditional name="tabular_annotation"> + <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots"> + <option value="no_annotation" selected="True">pixels belong into one group only</option> + <option value="yes_annotation">group pixels according to annotations</option> + </param> + <when value="yes_annotation"> + <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file" + help="Tabular file with three columns: x values, y values and pixel annotations"/> + <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> + <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> + <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> + <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </when> + <when value="no_annotation"/> + </conditional> <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"/> + <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/> + <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/> </repeat> </when> </conditional> @@ -473,10 +502,18 @@ </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 name="tabular_annotation"> + <param name="load_annotation" value="yes_annotation"/> + <param name="annotation_file" value="annotations.tabular" ftype="tabular"/> + <param name="column_x" value="1"/> + <param name="column_y" value="2"/> + <param name="column_names" value="4"/> + <param name="tabular_header" value="TRUE"/> + </conditional> + <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> @@ -523,8 +560,7 @@ - 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 the sample/each combined sample - +- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted - 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:
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations.tabular Tue Jul 24 04:53:42 2018 -0400 @@ -0,0 +1,10 @@ +X Y file_name column_name +1 1 file_one col1 +1 2 file_one col1 +1 3 file_one col1 +2 1 file_one col2 +2 2 file_one col2 +2 3 file_one col2 +3 1 file_one col3 +3 2 file_one col3 +3 3 file_one col3