| Previous changeset 11:d2596e1be091 (2020-10-06) Next changeset 13:c5aa9fca18c6 (2020-11-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty" |
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modified:
spectra_plots.xml |
| b |
| diff -r d2596e1be091 -r 10566783d718 spectra_plots.xml --- a/spectra_plots.xml Tue Oct 06 08:09:08 2020 +0000 +++ b/spectra_plots.xml Tue Nov 03 23:11:11 2020 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0"> +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1"> <description> mass spectrometry imaging mass spectra plots </description> @@ -82,7 +82,7 @@ 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 = as.factor(merged_annotation[,4]) + msidata\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order ## overview plot over annotated samples number_combined = length(levels(msidata\$annotation)) @@ -214,7 +214,7 @@ #if $fullmz: ## plot full mz for single tabular mz - print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable)) + print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable, col="black")) #end if pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord) @@ -261,7 +261,7 @@ } ## 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))) + 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")) #end for @@ -306,7 +306,7 @@ } ## print single tabular mz; tabular zoom - print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax))) + print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax), col="black")) } } @@ -329,7 +329,7 @@ #if $fullmz: - print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable)) + print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable, col="black")) #end if ##################### II) Sample: plot zoom-in mass spectrum ########## @@ -366,7 +366,7 @@ } } - print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))) + print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax), col="black")) #end for @@ -401,7 +401,7 @@ } ) - print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax))) + print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax), col="black")) } } |