Mercurial > repos > galaxyp > cardinal_spectra_plots
changeset 14:1693b2126f30 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 180894cfabbee2d308be140a0f0b4dba119e88d4-dirty"
| author | galaxyp |
|---|---|
| date | Wed, 23 Dec 2020 22:28:42 +0000 |
| parents | c5aa9fca18c6 |
| children | d333733dd571 |
| files | spectra_plots.xml test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/Plot_rdata.pdf |
| diffstat | 7 files changed, 23 insertions(+), 19 deletions(-) [+] |
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--- a/spectra_plots.xml Sun Nov 29 23:41:23 2020 +0000 +++ b/spectra_plots.xml Wed Dec 23 22:28:42 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.2"> +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.3"> <description> mass spectrometry imaging mass spectra plots </description> @@ -71,16 +71,23 @@ spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.single_or_overlaid.column_pixel_annotation)] colnames(spectra_input) = c("x", "y", "annotation") spectra_input\$annotation = as.character(spectra_input\$annotation) + + ## keeping only spectra with annotations + input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_") + dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_") + pixelsofinterest = dataset_pixels %in% input_pixels + msidata = msidata[,pixelsofinterest] - msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y) - colnames(msidata_coordinates) = c("x", "y") - merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y")) + msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata))) + colnames(msidata_coordinates) = c("x", "y", "pixel_index") + merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE) merged_annotation[is.na(merged_annotation)] = "NA" - - merged_annotation = merged_annotation[order(merged_annotation\$annotation),] - msidata\$annotation = factor(merged_annotation\$annotation) - - + merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),] + msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order + +print(msidata\$annotation) +print(merged_annotation) + ## overview plot over annotated samples number_combined = length(levels(msidata\$annotation)) @@ -105,15 +112,15 @@ #elif str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "colourpalette" - number_levels = (length(levels(msidata\$annotation))) - - colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels) + number_levels = (length(levels(msidata\$annotation))) + + colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels) #end if - - position_df = merged_annotation + + position_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, as.factor(msidata\$annotation)) colnames(position_df) = c("x", "y", "sample_name") - +print(position_df) combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ geom_tile(height = 1, width=1)+ coord_fixed()+ @@ -126,9 +133,8 @@ 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(unique(position_df\$sample_name)) + coord_labels\$file_number = 1:nrow(coord_labels) for(file_count in 1:nrow(coord_labels)) {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"], @@ -150,7 +156,6 @@ pixeldf = data.frame(table(msidata\$annotation)) colnames(pixeldf) = c("sample name", "number of pixels") - ##################### II) Sample: plot zoom-in mass spectrum ########## #if str($mz_range.mz_range_options) == "manual_mz": @@ -179,7 +184,6 @@ ) ## plot single tabular mz, average per annotation, manual zoom - print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, col = colourvector, xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable, key=key_legend, superpose=TRUE, main="Average spectrum per group"))