Mercurial > repos > galaxyp > msi_filtering
changeset 8:262db9893c6f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
| author | galaxyp |
|---|---|
| date | Wed, 22 Aug 2018 13:42:05 -0400 |
| parents | 73b5a754f35c |
| children | 28ac8199d4d5 |
| files | msi_filtering.xml test-data/analyze75_filtered2.pdf test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered2.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/rdata_notfiltered.pdf |
| diffstat | 15 files changed, 17 insertions(+), 2 deletions(-) [+] |
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--- a/msi_filtering.xml Wed Aug 15 05:40:01 2018 -0400 +++ b/msi_filtering.xml Wed Aug 22 13:42:05 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.5"> +<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.6"> <description>tool for filtering mass spectrometry imaging data</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> @@ -44,7 +44,12 @@ #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else - load('infile.RData') + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } + msidata = loadRData('infile.RData') + #end if @@ -392,6 +397,8 @@ { ### visual pixel control + levels(position_df\$annotation) = factor(paste(1:length(levels(position_df\$annotation)), levels(position_df\$annotation), sep="_")) + pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+ geom_tile(height = 1, width=1)+ coord_fixed()+ @@ -400,8 +407,16 @@ 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)) + coord_labels = aggregate(cbind(x,y)~annotation, data=position_df, mean, na.rm=TRUE, na.action="na.pass") + coord_labels\$file_number = 1:length(levels(position_df\$annotation)) + + for(file_count in 1:nrow(coord_labels)) + {pixel_image = pixel_image + annotate("text",x=coord_labels[file_count,"x"], + y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))} + print(pixel_image) ### control features which are removed