Mercurial > repos > galaxyp > cardinal_spectra_plots
changeset 13:c5aa9fca18c6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
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--- a/spectra_plots.xml Tue Nov 03 23:11:11 2020 +0000 +++ b/spectra_plots.xml Sun Nov 29 23:41:23 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1"> +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.2"> <description> mass spectrometry imaging mass spectra plots </description> @@ -66,23 +66,20 @@ ## read and extract x,y, optional annotation information spectra_tabular = read.delim("$pixel_conditional.pixel_file", header = $pixel_conditional.tabular_pixel_header, stringsAsFactors = FALSE) - #if $pixel_conditional.column_pixel_annotation: + #if str($pixel_conditional.single_or_overlaid.plot_type) == 'overlaid_plots': - spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.column_pixel_annotation)] + spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.single_or_overlaid.column_pixel_annotation)] colnames(spectra_input) = c("x", "y", "annotation") + spectra_input\$annotation = as.character(spectra_input\$annotation) - input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_") - dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_") - pixelsofinterest = dataset_pixels %in% input_pixels - msidata = msidata[,pixelsofinterest] + msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y) + colnames(msidata_coordinates) = c("x", "y") + merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y")) + merged_annotation[is.na(merged_annotation)] = "NA" - ## merge with coordinate information of msidata - msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata))) - colnames(msidata_coordinates) = c("x", "y", "pixel_index") - merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE) - merged_annotation[is.na(merged_annotation)] = "NA" - merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),] - msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order + merged_annotation = merged_annotation[order(merged_annotation\$annotation),] + msidata\$annotation = factor(merged_annotation\$annotation) + ## overview plot over annotated samples number_combined = length(levels(msidata\$annotation)) @@ -100,7 +97,21 @@ legend_size = 6 } - position_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, as.factor(msidata\$annotation)) + ## colours selection: + + #if str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "manual_colour" + #set $color_string = ','.join(['"%s"' % $color.annotation_color for $color in $pixel_conditional.single_or_overlaid.colour_conditional.colours]) + colourvector = c($color_string) + + #elif str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "colourpalette" + + number_levels = (length(levels(msidata\$annotation))) + + colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels) + + #end if + + position_df = merged_annotation colnames(position_df) = c("x", "y", "sample_name") combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ @@ -111,15 +122,18 @@ 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 = 6))+ - guides(fill=guide_legend(ncol=4,byrow=TRUE)) + theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 10))+ + guides(fill=guide_legend(ncol=4,byrow=TRUE))+ + scale_discrete_manual(aesthetics = c("colour", "fill"), values = colourvector) - coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass") - coord_labels\$file_number = 1:length(levels(position_df\$sample_name)) + + coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass") + coord_labels\$file_number = 1:length(unique(position_df\$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]))} + {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) @@ -130,7 +144,7 @@ #if $fullmz: ## plot single tabular mz, average per annotation - print(plot(msidata, run="infile", pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, strip=FALSE, grid=$grid_variable), main="Average spectrum per group") + print(plot(msidata, run="infile", pixel.groups=msidata\$annotation, key=key_legend,superpose=TRUE, strip=FALSE, grid=$grid_variable, col = colourvector), main="Average spectrum per group") #end if pixeldf = data.frame(table(msidata\$annotation)) @@ -165,9 +179,10 @@ ) ## plot single tabular mz, average per annotation, manual zoom - print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, + + print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, col = colourvector, xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, - key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE, main="Average spectrum per group")) + key=key_legend, superpose=TRUE, main="Average spectrum per group")) #end for #elif str($mz_range.mz_range_options) == "tabular_mz": @@ -186,17 +201,18 @@ ## plot single tabular mz, average per annotation, tabular zoom print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, main="Average spectrum per group", - xlim= c(xlimmin,xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, - key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE)) + xlim= c(xlimmin,xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, col = colourvector, + key=key_legend, superpose=TRUE)) + } } #end if + #elif str($pixel_conditional.single_or_overlaid.plot_type) == 'separate_plots': - #elif str($pixel_conditional.column_pixel_annotation)== "None": - spectra_tabular = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y)] - colnames(spectra_tabular) = c("x", "y") + spectra_tabular = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y)] + colnames(spectra_tabular) = c("x", "y") dataset_pixels = data.frame(coord(msidata)\$x, coord(msidata)\$y) colnames(dataset_pixels) = c("x", "y") @@ -261,7 +277,17 @@ } ## print single tabular mz; manual zoom - print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black")) + + tryCatch( + { + print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black")) + } + , + error=function(cond) { + ## if there are no intensities > 0 in the chosen plotting window, write a warning + text(0.5,0.5,labels = c(paste("No peaks in the spectrum with the coordinates x =", x_coord, ", y =", y_coord, sep=" "))) + } + ) #end for @@ -456,17 +482,53 @@ <expand macro="reading_msidata"/> <expand macro="pdf_filename"/> <conditional name="pixel_conditional"> - <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations"> - <option value="all_pixel" selected="True" >All spectra</option> - <option value="tabular_pixel">Single spectra</option> + <param name="pixel_type" type="select" label="Choose spectra"> + <option value="all_pixel" selected="True" >Plot mean spectra based on all spectra</option> + <option value="tabular_pixel">Plot single spectra (separate or overlaid)</option> </param> <when value="tabular_pixel"> <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates" help="Two or three columns: x values, y values, optionally annotations"/> <param name="column_pixel_x" data_ref="pixel_file" label="Column with x values" type="data_column"/> <param name="column_pixel_y" data_ref="pixel_file" label="Column with y values" type="data_column"/> - <param name="column_pixel_annotation" data_ref="pixel_file" optional="True" label="Column with annotations" type="data_column"/> <param name="tabular_pixel_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/> + <conditional name="single_or_overlaid"> + <param name="plot_type" type="select" label="Separate plot per spectrum or overlaid plot with average spectra per annotation group"> + <option value="separate_plots" selected="True" >Separate spectra plots</option> + <option value="overlaid_plots">Overlaid spectra plots</option> + </param> + <when value="separate_plots"/> + <when value="overlaid_plots"> + <param name="column_pixel_annotation" data_ref="pixel_file" label="Select column with annotations" type="data_column"/> + <conditional name="colour_conditional"> + <param name="colour_type" type="select" label="Choose a colour scheme"> + <option value="colourpalette" selected="True" >Colour palette</option> + <option value="manual_colour">Manual selection</option> + </param> + <when value="manual_colour"> + <repeat name="colours" title="Colours for the plots" min="1" max="50"> + <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + <when value="colourpalette"> + <param name="palettes" type="select" display="radio" label="Select a colourpalette"> + <option value="hue_pal()" selected="True">hue</option> + <option value="rainbow">rainbow</option> + <option value="heat.colors">heat colors</option> + <option value="terrain.colors">terrain colors</option> + <option value="topo.colors">topo colors</option> + <option value="cm.colors">cm colors</option> + </param> + </when> + </conditional> + </when> + </conditional> </when> <when value="all_pixel"> </when> @@ -554,19 +616,33 @@ <param name="pixel_file" value="annotations.tabular"/> <param name="column_pixel_x" value="1"/> <param name="column_pixel_y" value="2"/> - <param name="column_pixel_annotation" value="4"/> <param name="tabular_pixel_header" value="TRUE"/> + + <conditional name="single_or_overlaid"> + <param name="plot_type" value="overlaid_plots"/> + <param name="column_pixel_annotation" value="4"/> + <param name="colour_type" value="manual_colour"/> + <repeat name="colours"> + <param name="annotation_color" value="#0000FF"/> + </repeat> + <repeat name="colours"> + <param name="annotation_color" value="#00C957"/> + </repeat> + <repeat name="colours"> + <param name="annotation_color" value="#B0171F"/> + </repeat> + </conditional> </conditional> - <param name="fullmz" value="FALSE"/> - <conditional name="mz_range"> - <param name="mz_range_options" value="manual_mz"/> - <repeat name="zoomed_sample"> - <param name="xlimmin" value="1250"/> - <param name="xlimmax" value="1270"/> - </repeat> - </conditional> - <param name="grid_variable" value="FALSE"/> - <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/> + <param name="fullmz" value="FALSE"/> + <conditional name="mz_range"> + <param name="mz_range_options" value="manual_mz"/> + <repeat name="zoomed_sample"> + <param name="xlimmin" value="1250"/> + <param name="xlimmax" value="1270"/> + </repeat> + </conditional> + <param name="grid_variable" value="FALSE"/> + <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/> </test> <test> <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
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