| Previous changeset 6:bab12ded74a5 (2018-07-24) Next changeset 8:262db9893c6f (2018-08-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 620a469e20836b921b6c0147421c8a4268b66ebd |
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modified:
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 |
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removed:
test-data/inputcalibrantfile2.txt |
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| diff -r bab12ded74a5 -r 73b5a754f35c msi_filtering.xml --- a/msi_filtering.xml Tue Jul 24 04:52:54 2018 -0400 +++ b/msi_filtering.xml Wed Aug 15 05:40:01 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.4">\n+<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.5">\n <description>tool for filtering mass spectrometry imaging data</description>\n <requirements>\n <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>\n@@ -32,9 +32,8 @@\n \n \n library(Cardinal)\n+library(ggplot2)\n library(gridExtra)\n-library(ggplot2)\n-\n \n #if $infile.ext == \'imzml\'\n #if str($processed_cond.processed_file) == "processed":\n@@ -86,7 +85,7 @@\n \n ## prepare dataframe for QC of pixel distribution (will be overwritten in filtering of pixels condition)\n position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))\n-\n+ colnames(position_df)[3] = "annotation"\n \n ###################################### Filtering of pixels #####################\n ################################################################################\n@@ -103,6 +102,7 @@\n valid_entries = input_list[startingrow:nrow(input_list),$pixels_cond.pixel_column] %in% names(pixels(msidata))\n validpixels = sum(valid_entries)\n valid_annotations = input_list[valid_entries,c($pixels_cond.pixel_column, $pixels_cond.annotation_column)]\n+ colnames(valid_annotations) = c("pixel_coordinates", "annotation")\n \n ## for valid pixels: filter file for pixels and create dataframe with x,y,annotation for QC\n if (validpixels != 0){\n@@ -110,8 +110,16 @@\n pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% valid_annotations[,1]]\n msidata = msidata[,pixelsofinterest]\n ## position_df for QC\n- pixel_coords = coord(msidata)[names(pixels(msidata)) %in% valid_annotations[,1],1:2]\n- position_df = cbind(pixel_coords, valid_annotations[,2])\n+\n+\n+ ###pixel_coords = coord(msidata)[names(pixels(msidata)) %in% valid_annotations[,1],1:2]\n+ pixel_coords = cbind(rownames(coord(msidata)), coord(msidata))\n+ colnames(pixel_coords)[1] = "pixel_coordinates"\n+\n+ ###position_df = cbind(pixel_coords, valid_annotations[,2])\n+ position_df = merge(pixel_coords, valid_annotations)\n+ position_df\\$annotation = factor(position_df\\$annotation)\n+\n }else{\n msidata = msidata[,0]\n validpixels=0}\n@@ -129,8 +137,9 @@\n inputpixels = input_list[startingrow:nrow(input_list),c($pixels_cond.pixel_column_x, $pixels_cond.pixel_column_y, $pixels_cond.annotation_column_xy)]\n colnames(inputpixels) = c("x", "y", "annotation")\n position_df = merge(coord(msidata)[,1:2], inputpixels, by=c("x", "y"), all.x=TRUE)\n-\n validpixels = nrow(position_df)\n+ colnames(position_df)[3] = "annotation"\n+ position_df\\$annotation = factor(position_df\\$annotation)\n \n ## for valid pixels: filter file for pixels\n if (validpixels != 0){\n@@ -159,6 +168,11 @@\n msidata = msidata[,0]\n print("no valid pixel found")}\n \n+ ## update position_df for filtered pixels\n+ position_df = cbind(coord(msidata)[,1:2], rep("$infile.element_identifier", times=ncol(msidata)))\n+ colnames(position_df)[3] = "annotation"\n+ position_df\\$annotation = factor(position_df\\$annotation)\n+\n #elif str($pixels_cond.pixel_filtering) == "none":\n print("no pixel filtering")\n \n@@ -177,7 +191,12 @@\n ####################### Keep m/z from tabular file #########################\n \n ## feature filtering only when pixels/features/intensities are left\n-if (sum(spectra(msidata)[], na.rm=TRUE) > 0)\n+ npeaks_before_filtering= sum(spectra(msidata)[]>0, na.rm=TRUE)\n+\n+\n+\n+if (npeaks_before_filtering > 0)\n+\n {\n \n #if str($features_cond.features_filtering) == "features_list":\n@@ -369,21 +388,19 @@\n grid.table(property_df, rows= NULL)\n \n ## QC report with '..b'- pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation_name))+\n- geom_tile() +\n+ pixel_image = ggplot(position_df, aes(x=x, y=y, fill=annotation))+\n+ geom_tile(height = 1, width=1)+\n coord_fixed()+\n- ggtitle("Spatial orientation of combined data")+\n+ ggtitle("Spatial orientation of filtered pixels")+\n theme_bw()+\n- theme(text=element_text(family="ArialMT", face="bold", size=15))+\n+ theme(plot.title = element_text(hjust = 0.5))+\n+ theme(text=element_text(family="ArialMT", face="bold", size=12))+\n theme(legend.position="bottom",legend.direction="vertical")+\n guides(fill=guide_legend(ncol=4,byrow=TRUE))\n- coord_labels = aggregate(cbind(x,y)~annotation_name, data=position_df, mean, na.rm=TRUE, na.action="na.pass")\n- coord_labels\\$file_number = gsub( "_.*$", "", coord_labels\\$annotation_name)\n \n print(pixel_image)\n \n@@ -515,12 +532,13 @@\n <param name="pixel_filtering" value="single_column"/>\n <param name="single_pixels" ftype="tabular" value = "inputpixels.tabular"/>\n <param name="pixel_column" value="1"/>\n+ <param name="annotation_column" value="2"/>\n <param name="features_filtering" value="features_list"/>\n <param name="inputfeatures" ftype="tabular" value = "inputfeatures.tabular"/>\n <param name="feature_column" value="2"/>\n <param name="feature_header" value="1"/>\n <output name="filtering_qc" file="imzml_filtered.pdf" compare="sim_size" delta="20000"/>\n- <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size" />\n+ <output name="msidata_filtered" file="imzml_filtered.RData" compare="sim_size"/>\n </test>\n <test expect_num_outputs="2">\n <param name="infile" value="" ftype="imzml">\n@@ -533,7 +551,7 @@\n <param name="min_y_range" value="2"/>\n <param name="max_y_range" value="2"/>\n <output name="filtering_qc" file="imzml_filtered2.pdf" compare="sim_size" delta="20000"/>\n- <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size" />\n+ <output name="msidata_filtered" file="imzml_filtered2.RData" compare="sim_size"/>\n </test>\n <test expect_num_outputs="3">\n <param name="infile" value="" ftype="imzml">\n@@ -550,7 +568,7 @@\n <param name="max_mz" value="500"/>\n <param name="output_matrix" value="True"/>\n <output name="filtering_qc" file="imzml_filtered3.pdf" compare="sim_size" delta="20000"/>\n- <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size" />\n+ <output name="msidata_filtered" file="imzml_filtered3.RData" compare="sim_size"/>\n <output name="matrixasoutput" file="imzml_matrix3.tabular"/>\n </test>\n <test expect_num_outputs="2">\n@@ -563,12 +581,8 @@\n <param name="pixel_column_x" value="1"/>\n <param name="pixel_column_y" value="3"/>\n <param name="annotation_column_xy" value="2"/>\n- <param name="features_filtering" value="features_list"/>\n- <param name="inputfeatures" ftype="tabular" value = "inputcalibrantfile2.txt"/>\n- <param name="feature_column" value="1"/>\n- <param name="feature_header" value="0"/>\n <output name="filtering_qc" file="imzml_filtered4.pdf" compare="sim_size" delta="20000"/>\n- <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size" />\n+ <output name="msidata_filtered" file="imzml_filtered4.RData" compare="sim_size"/>\n </test>\n <test expect_num_outputs="2">\n <param name="infile" value="" ftype="imzml">\n' |
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| diff -r bab12ded74a5 -r 73b5a754f35c test-data/inputcalibrantfile2.txt --- a/test-data/inputcalibrantfile2.txt Tue Jul 24 04:52:54 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -869.51 mass1 -1001.62 mass2 -1023.6 mass3 |
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