# HG changeset patch # User galaxyp # Date 1606692181 0 # Node ID a2b57ea6666ed2ecf3ef815b6e9b1d0f7909aa01 # Parent a95a82eb4d50c36cbe907ff80c8e3c17c30be72f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" diff -r a95a82eb4d50 -r a2b57ea6666e mz_images.xml --- a/mz_images.xml Wed Oct 21 22:58:11 2020 +0000 +++ b/mz_images.xml Sun Nov 29 23:23:01 2020 +0000 @@ -1,4 +1,4 @@ - + mass spectrometry imaging m/z heatmaps @@ -62,12 +62,19 @@ ### only plot images when file has features and pixels: par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend + +#if str($light_mode) == "white": + lightmode() +#else + darkmode() +#end if + if (ncol(msidata)>0 & nrow(msidata) >0){ if (length(inputmz) != 0){ for (mass in 1:length(inputmz)){ print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", - smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy))) + smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy))) title(inputnames[mass], adj = 0.5, line = 1)} @@ -81,7 +88,12 @@ svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg - print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", normalize.image="$normalize_image")) + #if str($light_mode) == "white": + lightmode() + #else + darkmode() + #end if + print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", alpha.power=$alpha_power, normalize.image="$normalize_image")) dev.off() #end if @@ -90,15 +102,14 @@ #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours]) colourvector = c($color_string) - par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend print(image(msidata, mz=inputmz, plusminus = $plusminus_dalton, - col=colourvector, + col=colourvector, contrast.enhance = "$image_contrast", normalize.image="$normalize_image", smooth.image = "$image_smoothing", superpose=TRUE, main="overlay of all m/z", - key=FALSE, + key=FALSE, alpha.power=$alpha_power, ylim= c(maximumy,minimumy))) legend("$overlay_cond.legend_position", @@ -121,7 +132,7 @@ - + @@ -138,6 +149,11 @@ + + + + + @@ -233,6 +249,7 @@ + diff -r a95a82eb4d50 -r a2b57ea6666e test-data/Heatmaps_LM8_file16.pdf Binary file test-data/Heatmaps_LM8_file16.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/Heatmaps_analyze75.pdf Binary file test-data/Heatmaps_analyze75.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/Heatmaps_imzml.pdf Binary file test-data/Heatmaps_imzml.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/Heatmaps_processed.pdf Binary file test-data/Heatmaps_processed.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/Heatmaps_rdata.pdf Binary file test-data/Heatmaps_rdata.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/centroids_proc.pdf Binary file test-data/centroids_proc.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.ibd Binary file test-data/preprocessing_results1.ibd has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Sun Nov 29 23:23:01 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -86,15 +86,15 @@ - - + + - - - + + + @@ -115,15 +115,15 @@ - - + + - - - + + + @@ -144,15 +144,15 @@ - - + + - - - + + + @@ -173,15 +173,15 @@ - - + + - - - + + + @@ -202,15 +202,15 @@ - - + + - - - + + + @@ -231,15 +231,15 @@ - - + + - - - + + + @@ -260,15 +260,15 @@ - - + + - - - + + + @@ -289,15 +289,15 @@ - - + + - - - + + + @@ -318,15 +318,15 @@ - - + + - - - + + + diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Sun Nov 29 23:23:01 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 336 Nov 29 01:14 ibd +-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results1.pdf Binary file test-data/preprocessing_results1.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.ibd Binary file test-data/preprocessing_results2.ibd has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Sun Nov 29 23:23:01 2020 +0000 @@ -9,8 +9,8 @@ - - + + diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Sun Nov 29 23:23:01 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 64 --rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd +-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results2.pdf Binary file test-data/preprocessing_results2.pdf has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.ibd Binary file test-data/preprocessing_results3.ibd has changed diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Sun Nov 29 23:23:01 2020 +0000 @@ -9,9 +9,9 @@ - - - + + + @@ -86,15 +86,15 @@ - - + + - - - + + + @@ -114,16 +114,16 @@ - - - + + + - - - + + + @@ -143,16 +143,16 @@ - - - + + + - - - + + + @@ -172,16 +172,16 @@ - - - + + + - - - + + + @@ -201,16 +201,16 @@ - - - + + + - - - + + + @@ -230,16 +230,16 @@ - - - + + + - - - + + + @@ -259,16 +259,16 @@ - - - + + + - - - + + + @@ -288,16 +288,16 @@ - - - + + + - - - + + + @@ -317,16 +317,16 @@ - - - + + + - - - + + + diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Wed Oct 21 22:58:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Sun Nov 29 23:23:01 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 960 Oct 5 19:58 ibd --rw-rw-r-- 1 meli meli 18112 Oct 5 19:58 imzml +-rw-rw-r-- 1 meli meli 1456 Nov 29 18:04 ibd +-rw-rw-r-- 1 meli meli 18133 Nov 29 18:04 imzml diff -r a95a82eb4d50 -r a2b57ea6666e test-data/preprocessing_results3.pdf Binary file test-data/preprocessing_results3.pdf has changed