| Next changeset 1:53a2f4fa6cd2 (2023-04-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit badc51fcd74ba0c14cd1ae64d5f524291fa11441" |
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added:
macros.xml spatial_DGMM.xml static/images/classification_overview.png test-data/112_annotation_output.tabular test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/112_auto_combined_QC.pdf test-data/123_annotation.ibd test-data/123_annotation.imzml test-data/123_annotation.tabular test-data/123_annotation_output.tabular test-data/123_auto_combined.imzml.txt test-data/123_combine.rdata test-data/123_combined.RData test-data/123_combined.ibd test-data/123_combined.imzml test-data/123_combined.imzml.txt test-data/123_combined_QC.pdf test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/123_combined_auto.tabular test-data/123_combined_picked.rdata test-data/123_combined_picked2.rdata test-data/12_annotation_output.tabular test-data/12_combined.ibd test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/12_combined_QC.pdf test-data/2123_annotation_output.tabular test-data/2123_auto_combined.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf test-data/3_files_combined.RData test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/DGMM_annotations.tabular test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/Example_Processed.ibd test-data/Example_Processed.imzML test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf 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 test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_imzml_shortreport.pdf test-data/QC_rdata.pdf test-data/analyze75.svg test-data/analyze75_filtered2.pdf test-data/annotations.tabular test-data/annotations_file1.tabular test-data/annotations_file2.tabular test-data/annotations_file3.tabular test-data/annotations_rdata.tabular test-data/centroids_proc.pdf test-data/centroids_rdata.pdf test-data/classes_proc.tabular test-data/classes_ssc.tabular test-data/cluster_skm.RData test-data/cluster_skm.tabular test-data/coloc1.pdf test-data/coloc2.pdf test-data/coloc3.pdf test-data/coloc_table1.tabular test-data/coloc_table2.tabular test-data/coloc_table3.tabular test-data/dgmm_summary1.tabular test-data/dgmm_summary2.tabular test-data/dgmm_test1.pdf test-data/dgmm_test2.RData test-data/dgmm_test2.pdf test-data/empty_spectra.rdata test-data/estimates_r1_k6_mz1135.93347167969.tabular test-data/estimates_r2_k10_mz1200.46533203125.tabular test-data/features_out1.tabular test-data/features_out3.tabular test-data/features_out4.tabular test-data/features_test1.tabular test-data/features_test2.tabular test-data/features_test3.tabular test-data/features_test4.tabular test-data/features_test5.tabular test-data/features_test6.tabular test-data/features_test7.tabular test-data/featuresofinterest5.tabular test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf test-data/inputcalibrantfile1.tabular test-data/inputcalibrantfile2.txt test-data/inputpeptides.tabular test-data/inputpeptides2.tabular test-data/inputpixels_2column.tabular test-data/int_matrix1.tabular test-data/int_matrix3.tabular test-data/kmeans_analyze.pdf test-data/mean_out2.tabular test-data/msidata_1.RData test-data/msidata_2.RData test-data/msidata_3.RData test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/pca_imzml.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked.tabular test-data/picked_QC.pdf test-data/pixel_annotation_file1.tabular test-data/pixel_out2.tabular test-data/pixel_out3.tabular test-data/pixel_out4.tabular test-data/pixels_test1.tabular test-data/pixels_test2.tabular test-data/pixels_test3.tabular test-data/pixels_test4.tabular test-data/pixels_test5.tabular test-data/pixels_test6.tabular test-data/pixels_test7.tabular test-data/preprocessed.RData test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt test-data/preprocessing_results5.pdf test-data/probability_r1_k6_mz1023.70806884766.tabular test-data/probability_r2_k10_mz1135.93347167969.tabular test-data/random_factors.tabular test-data/rdata_notfiltered.pdf test-data/scores_pca.tabular test-data/sd_out2.tabular test-data/spatial_DGMM_input.ibd test-data/spatial_DGMM_input.imzML test-data/spectra_1_pixel.tabular test-data/spectra_info_123_combi.txt test-data/spectra_info_imzml.txt test-data/tabular_LM8file16.tabular test-data/tabular_analyze75.tabular test-data/tabular_imzml.tabular test-data/tabular_rdata.tabular test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata test-data/testfile_squares.rdata test-data/toplabels_proc.tabular test-data/toplabels_skm.tabular test-data/toplabels_ssc.tabular test-data/xy_coordinates.tabular test-data/xy_coordinates2.tabular |
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| diff -r 000000000000 -r 4cb6c83d3777 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Feb 22 20:51:09 2022 +0000 |
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| b'@@ -0,0 +1,328 @@\n+<macros>\n+ <token name="@VERSION@">2.10.0</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>\n+ <!--requirement type="package" version="3.6.1">r-base</requirement-->\n+ <yield/>\n+ </requirements>\n+ </xml>\n+\n+ <xml name="print_version">\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\\$otherPkgs\\$Cardinal\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ </xml>\n+\n+ <token name="@INPUT_LINKING@"><![CDATA[\n+ #if $infile.ext == \'imzml\'\n+ ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ #elif $infile.ext == \'analyze75\'\n+ ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\n+ ln -s \'${infile.extra_files_path}/img\' infile.img &&\n+ ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\n+ #else\n+ ln -s $infile infile.RData &&\n+ #end if\n+ ]]></token>\n+\n+\n+ <token name="@READING_MSIDATA@"><![CDATA[\n+ ## importing MSI data files\n+\n+ ## read RData files (MSI and other data) independent of filename\n+ loadRData <- function(fileName){\n+ load(fileName)\n+ get(ls()[ls() != "fileName"])\n+ }\n+\n+ #if $infile.ext == \'imzml\'\n+ #if str($processed_cond.processed_file) == "processed":\n+ msidata <- readImzML(\'infile\', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")\n+ msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous\n+ centroided(msidata) = $centroids\n+ #else\n+ msidata <- readImzML(\'infile\', attach.only=TRUE)\n+ centroided(msidata) = $centroids\n+ #end if\n+ #elif $infile.ext == \'analyze75\'\n+ msidata = readAnalyze(\'infile\', attach.only=TRUE)\n+ centroided(msidata) = $centroids\n+ #else\n+ msidata = loadRData(\'infile.RData\')\n+ #end if\n+\n+ ]]></token>\n+\n+ <token name="@DATA_PROPERTIES@"><![CDATA[\n+ ## Number of features (mz)\n+ maxfeatures = length(features(msidata))\n+ ## Range mz\n+ minmz = round(min(mz(msidata)), digits=2)\n+ maxmz = round(max(mz(msidata)), digits=2)\n+ ## Number of spectra (pixels)\n+ pixelcount = length(pixels(msidata))\n+ ## Range x coordinates\n+ minimumx = min(coord(msidata)[,1])\n+ maximumx = max(coord(msidata)[,1])\n+ ## Range y coordinates\n+ minimumy = min(coord(msidata)[,2])\n+ maximumy = max(coord(msidata)[,2])\n+\n+\n+ properties = c("Number of m/z features",\n+ "Range of m/z values",\n+ "Number of pixels", \n+ "Range of x coordinates", \n+ "Range of y coordinates")\n+\n+ values = c(paste0(maxfeatures), \n+ paste0(minmz, " - ", maxmz), \n+ paste0(pixelcount), \n+ paste0(minimumx, " - ", maximumx),\n+ paste0(minimumy, " - ", maximumy))\n+\n+ property_df = data.frame(properties, values)\n+ ]]></token>\n+\n+ <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![CDATA[\n+ ## importing MSI data files\n+\n+ #if $infile.ext == \'imzml\'\n+ #if str($processed_cond.processed_file) == "processed":\n+ msidata <- readImzML(\'infile\', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)\n+ centroided(msidata) = $centroids\n+ #else\n+ msidata <- readImzML(\'infile\', attach.only=TRUE)\n+ centroided(msidata) = $centroids\n'..b' or ppm">\n+ <option value="mz" >mz</option>\n+ <option value="ppm" selected="True" >ppm</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="pdf_filename">\n+ <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_"/>\n+ <add value=" "/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </xml>\n+\n+ <xml name="sanitizer_multiple_digits">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.digits">\n+ <add value=":" />\n+ <add value="," />\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+\n+ <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">\n+ <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>\n+ <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>\n+ <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="reading_2_column_mz_tabular" token_optional="false">\n+ <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"\n+ label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>\n+ <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>\n+ <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>\n+ <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="reading_pixel_annotations">\n+ <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"\n+ help="Tabular file with three columns: x values, y values and pixel annotations"/>\n+ <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>\n+ <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>\n+ <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>\n+ <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ <citation type="doi">10.1093/gigascience/giz143</citation>\n+ </citations>\n+ </xml>\n+ <xml name="infile_analyze75">\n+ <param name="infile" value="" ftype="analyze75">\n+ <composite_data value="Analyze75.hdr"/>\n+ <composite_data value="Analyze75.img"/>\n+ <composite_data value="Analyze75.t2m"/>\n+ </param>\n+ </xml>\n+ <xml name="infile_imzml">\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Continuous.imzML"/>\n+ <composite_data value="Example_Continuous.ibd"/>\n+ </param>\n+ </xml>\n+ <xml name="processed_infile_imzml">\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Processed.imzML"/>\n+ <composite_data value="Example_Processed.ibd"/>\n+ </param>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 4cb6c83d3777 spatial_DGMM.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spatial_DGMM.xml Tue Feb 22 20:51:09 2022 +0000 |
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| b'@@ -0,0 +1,309 @@\n+<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0">\n+ <description>mass spectrometry imaging spatial DGMM</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.3">r-gridextra</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ @INPUT_LINKING@\n+ cat \'${MSI_spatial_DGMM}\' &&\n+ Rscript \'${MSI_spatial_DGMM}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_spatial_DGMM"><![CDATA[\n+\n+################################# load libraries and read file #################\n+\n+library(Cardinal)\n+library(gridExtra)\n+\n+@READING_MSIDATA_FULLY_COMPATIBLE@\n+\n+#if str($sample_groups.group) == "multiple_groups":\n+ ## read and extract x,y,annotation information\n+ input_tabular <- read.delim("$sample_groups.annotation_file", header = $sample_groups.tabular_header, stringsAsFactors = FALSE)\n+ annotation_input <- input_tabular[,c($sample_groups.column_x, $sample_groups.column_y, $sample_groups.column_names)]\n+ annotation_name <- colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name\n+ colnames(annotation_input) <- c("x", "y", "annotation") ## rename annotations header to default name "annotation"\n+\n+ ## merge with coordinate information of msidata\n+ msidata_coordinates <- data.frame(coord(msidata)\\$x, coord(msidata)\\$y, c(1:ncol(msidata)))\n+ colnames(msidata_coordinates) <- c("x", "y", "pixel_index")\n+ merged_annotation <- merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)\n+ merged_annotation[is.na(merged_annotation)] <- "NA"\n+ merged_annotation <- merged_annotation[order(merged_annotation\\$pixel_index),]\n+ msidata\\$annotation <- as.character(merged_annotation[,4])\n+#end if\n+\n+\n+@DATA_PROPERTIES_INRAM@\n+\n+\n+## remove duplicated coordinates\n+msidata <- msidata[,!duplicated(coord(msidata))]\n+\n+\n+######################################## PDF ###################################\n+################################################################################\n+################################################################################\n+\n+\n+pdf("single_ion_segmentation.pdf", fonts = "Times", pointsize = 12)\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n+\n+title(main=paste0("Single ion segmentation for file: \\n\\n", "$infile.display_name"))\n+\n+grid.table(property_df, rows= NULL)\n+\n+if (npeaks > 0)\n+{\n+ \n+ ## set seed to make analysis reproducible\n+ set.seed($setseed)\n+ \n+\n+ ## single ion segmentation\n+ dgmm <- spatialDGMM(msidata, \n+ r = c($r),\n+ k = c($k), \n+ #if str($sample_groups.group) == \'single_group\': \n+ groups = as.factor(rep("$infile.display_name", ncol(msidata))),\n+ #else\n+ groups = msidata\\$annotation, \n+ #end if\n+ method = "$method",\n+ dist = "$dist", \n+ annealing = $annealing,\n+ init = "$init", \n+ p0 = $p0,\n+ iter.max = $iter_max, \n+ tol = $tol)\n+ \t \n+ ## Summary results table\n+ dgmm_summary <- as.data.frame(summary(dgmm))\n+ colnames(dgmm_summary) <- c(\'r\', \'k\', \'Feature\', \'Classes/group\')\n+ dgmm_summary\\$\'m/z\' <- mz(msidata)\n+ feature_n <- dgmm_summary\\$Feature\n+ dgmm_summary\\$Feature <- NULL\n+ dgmm_summary\\$Feature <- feature_n\n+ write.table(dgmm_summary, file="$dgmm_summary", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\\t")\n+ \n+ ## Results images\n+ for (dgmm_repeat in 1:nrow(dgmm_summary)){\n+ \tprint(image(dgmm, values="class", model=dgmm_repeat))}\n+ dev.off() ## closes pdf file\n+ \n+ ## optional outputs\n+ pixel_names <- paste0("xy_", coord(dgmm)\\$x, "_", coord(dgmm)\\$y)\n+\n+ #if $output_probabili'..b'le_groups"/>\n+ <param name="annotation_file" value="DGMM_annotations.tabular"/>\n+ <param name="column_x" value="1"/>\n+ <param name="column_y" value="2"/>\n+ <param name="column_names" value="3"/>\n+ <param name="tabular_header" value="True"/>\n+ </conditional>\n+ <param name="r" value="2"/>\n+\t<param name="k" value="10"/> \n+\t<param name="annealing" value="TRUE"/>\n+ <param name="output_estimates" value="True"/>\n+ <param name="output_probability" value="True"/>\n+ <param name="output_plots" value="True"/>\n+ <param name="output_rdata" value="True"/>\n+ <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/>\n+ <output name="dgmm_summary" file="dgmm_summary2.tabular"/>\n+ <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/>\n+ <output_collection name="estimates_output" type="list" count="10">\n+ <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/>\n+ </output_collection>\n+ <output_collection name="probability_output" type="list" count="10">\n+ <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/>\n+ </output_collection>\n+ </test> \n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool fits spatially-aware Dirichlet Gaussian mixture models (DGMM) to each feature and each run in an mass spectrometry imaging\n+experiment. Each image is segmented and the means and variances of all Gaussian components are estimated. A linear filter with a spatial kernel is applied to the component probabilities to achieve\n+spatial smoothing. Simulated annealing is used in the EM-algorithm to avoid local optima and achieve more accurate parameter estimates.\n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+ - NA intensities are not allowed\n+ - duplicated coordinates will be removed\n+ - It is highly recommended to use a dataset that is reduced for the number of m/z features e.g. pre-processed, binned, filtered for m/z of interest in order to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool). \n+\n+@SPECTRA_TABULAR_INPUT_DESCRIPTION@\n+\n+**Tips**\n+\n+- The input dataset should contain as few m/z features as possible to keep computational times reasonable. In addition, it is beneficial to run the tool first without generating all possible results data and upon inspection of the summary of the results decide on the best tool parameters and m/z features (which can be filtered in the MSI filtering tool). \n+- Pixels from distinct ovbservational units (e.g. sample, patient) should be assigned to a unique group via the annotation file and segmented separately for the validity of downstream statistical analysis. \n+\n+**Output**\n+\n+- Pdf with file info and an image of the clusters for each m/z feature\n+- Tabular file summarizing spatial DGMM performance for each feature\n+- (optional) Tabular files for each spatial DGMM run and feature with\n+\n+ - probabilities (The probability of class membership for each Gaussian component) and classes (The predicted Gaussian component)\n+ - estimates (A list giving the parameter estimates for the means and variances for each Gaussian component)\n+- (optional) Visualization of features density plots \n+- (optional) .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ <citation type="doi">10.1093/bioinformatics/btz345</citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 4cb6c83d3777 test-data/112_annotation_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/112_annotation_output.tabular Tue Feb 22 20:51:09 2022 +0000 |
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| @@ -0,0 +1,16 @@ +x y sample_name file_name column_name +1 1 msidata_1.RData file_one col1 +1 2 msidata_1.RData file_one col1 +1 3 msidata_1.RData file_one col1 +7 1 123_combined.RData file_one col1 +7 2 123_combined.RData file_one col1 +7 3 123_combined.RData file_one col1 +9 1 123_combined.RData file_two col2 +10 1 123_combined.RData file_two col3 +9 2 123_combined.RData file_two col2 +10 2 123_combined.RData file_two col3 +9 3 123_combined.RData file_two col2 +10 3 123_combined.RData file_two col3 +15 1 123_combined.RData file_three col3 +15 2 123_combined.RData file_three col3 +15 3 123_combined.RData file_three col3 |
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| b |
| b'@@ -0,0 +1,1200 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t397.083343505859\t0.032068928082784\t0\t0.0962067842483521\t300\t0.288620352745056\t2\n+mz_397.166687011719\t397.166687011719\t0.0199043717649248\t0\t0.0597131152947744\t300\t0.179139345884323\t2\n+mz_397.25\t397.25\t0.00360411198602782\t0\t0.0108123359580835\t300\t0.0324370078742504\t2\n+mz_397.333343505859\t397.333343505859\t5.81765407613358e-19\t0\t1.74529622283953e-18\t299.999999999906\t5.23588866852022e-18\t2\n+mz_397.416687011719\t397.416687011719\t1.46372722807492e-19\t0\t4.39118168421406e-19\t299.999999999268\t1.31735450526743e-18\t2\n+mz_397.5\t397.5\t7.38184882329827e-21\t0\t2.21455464696484e-20\t299.999999996662\t6.64366394096844e-20\t2\n+mz_397.583343505859\t397.583343505859\t5.19108733658977e-23\t0\t1.55732620090041e-22\t299.99999998526\t4.67197860293079e-22\t2\n+mz_397.666687011719\t397.666687011719\t2.15759913165433e-06\t0\t6.47279739496298e-06\t300\t1.94183921848889e-05\t2\n+mz_397.75\t397.75\t6.33312184719317e-07\t0\t1.89993655415795e-06\t300\t5.69980966247385e-06\t2\n+mz_397.833343505859\t397.833343505859\t5.05598304951289e-08\t0\t1.51679491485387e-07\t300\t4.5503847445616e-07\t2\n+mz_397.916687011719\t397.916687011719\t2.1973092932285e-23\t0\t6.59192787967557e-23\t299.999999999548\t1.97757836390565e-22\t2\n+mz_398\t398\t3.04395583748723e-24\t0\t9.13186751242318e-24\t299.999999998735\t2.73956025373851e-23\t2\n+mz_398.083343505859\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n+mz_398.166687011719\t398.166687011719\t0.0476158229749465\t0\t0.142847468396982\t299.999998891423\t0.428542406774519\t3\n+mz_398.25\t398.25\t0.0337751011944952\t0\t0.101325303282695\t299.999999109431\t0.303975910750457\t3\n+mz_398.333343505859\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n+mz_398.416687011719\t398.416687011719\t0\t0\t0\tNA\t0\t0\n+mz_398.5\t398.5\t1.45001195853997e-39\t0\t4.35003587561991e-39\t300\t1.30501076268597e-38\t1\n+mz_398.583343505859\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n+mz_398.666687011719\t398.666687011719\t0.00365118661688434\t0\t0.0075229081301236\t206.040088319099\t0.032860679551959\t3\n+mz_398.75\t398.75\t0.0974471403492822\t0\t0.218609809238247\t224.336813224769\t0.877024263143539\t3\n+mz_398.833343505859\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n+mz_398.916687011719\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n+mz_399\t399\t0\t0\t0\tNA\t0\t0\n+mz_399.083343505859\t399.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.166687011719\t399.166687011719\t2.12591405853366e-35\t0\t6.37774217560099e-35\t300\t1.9133226526803e-34\t1\n+mz_399.25\t399.25\t8.92074257340149e-36\t0\t2.67622277202045e-35\t300\t8.02866831606135e-35\t1\n+mz_399.333343505859\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n+mz_399.416687011719\t399.416687011719\t2.75656642164298e-06\t0\t6.22119222208426e-06\t225.686280339158\t2.48090977947868e-05\t2\n+mz_399.5\t399.5\t2.66098109275643e-07\t0\t6.10309301715427e-07\t229.354993681382\t2.39488298348078e-06\t2\n+mz_399.583343505859\t399.583343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.666687011719\t399.666687011719\t0\t0\t0\tNA\t0\t0\n+mz_399.75\t399.75\t0\t0\t0\tNA\t0\t0\n+mz_399.833343505859\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n+mz_399.916687011719\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n' |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/features_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_out4.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| b'@@ -0,0 +1,10399 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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/features_test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test2.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/features_test4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test4.tabular Tue Feb 22 20:51:09 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/features_test6.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test6.tabular Tue Feb 22 20:51:09 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/features_test7.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test7.tabular Tue Feb 22 20:51:09 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/featuresofinterest5.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featuresofinterest5.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,31 @@ +115.333335876465 +115.416664123535 +115.5 +115.583335876465 +115.666664123535 +115.75 +115.833335876465 +115.916664123535 +116 +116.083335876465 +116.166664123535 +116.25 +116.333335876465 +116.416664123535 +116.5 +116.583335876465 +116.666664123535 +319.083343505859 +319.166687011719 +319.25 +319.333343505859 +319.416687011719 +319.5 +319.583343505859 +319.666687011719 +319.75 +319.8 +319.916687011719 +320 +320.0833435 +350 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/imzml_filtered3.pdf |
| b |
| Binary file test-data/imzml_filtered3.pdf has changed |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/imzml_filtered4.pdf |
| b |
| Binary file test-data/imzml_filtered4.pdf has changed |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/imzml_filtered5.pdf |
| b |
| Binary file test-data/imzml_filtered5.pdf has changed |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/imzml_filtered8.pdf |
| b |
| Binary file test-data/imzml_filtered8.pdf has changed |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/inputcalibrantfile1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile1.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +101.5 +356.7 +555.1 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/inputcalibrantfile2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile2.txt Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +869.51 mass1 +1111.1 mass2 +1296.7 mass3 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/inputpeptides.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/inputpeptides2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides2.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +854.5 +1111.1 +1296.7 +1305.1 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/inputpixels_2column.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels_2column.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +1 A 1 +1 B 2 +1 C 3 +3 D 1 +3 E 2 +30 F 3 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/int_matrix1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_matrix1.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| b'@@ -0,0 +1,1200 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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/int_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_matrix3.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
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| diff -r 000000000000 -r 4cb6c83d3777 test-data/mean_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mean_out2.tabular Tue Feb 22 20:51:09 2022 +0000 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 192 +-rw-rw-r-- 1 meli meli 157984 Aug 30 13:47 ibd +-rw-rw-r-- 1 meli meli 35012 Aug 30 13:47 imzml |
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| @@ -0,0 +1,19 @@ +x y sample_name +1 1 File1 +1 2 File1 +1 3 File1 +3 1 File1 +4 1 File1 +3 2 File1 +4 2 File1 +3 3 File1 +4 3 File1 +11 1 File2 +12 1 File2 +11 2 File2 +12 2 File2 +11 3 File2 +12 3 File2 +17 1 File2 +17 2 File2 +17 3 File2 |
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| diff -r 000000000000 -r 4cb6c83d3777 test-data/picked_QC.pdf |
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| @@ -0,0 +1,24 @@ +1 1 Fold1 A +2 1 Fold1 A +3 1 Fold1 A +4 1 Fold1 A +1 2 Fold1 B +2 2 Fold1 B +3 2 Fold1 B +4 2 Fold1 B +1 3 Fold1 C +2 3 Fold1 C +3 3 Fold1 C +4 3 Fold1 C +10 1 Fold2 A +11 1 Fold2 A +12 1 Fold2 A +13 1 Fold2 A +10 2 Fold2 B +11 2 Fold2 B +12 2 Fold2 B +13 2 Fold2 B +10 3 Fold2 C +11 3 Fold2 C +12 3 Fold2 C +13 3 Fold2 C |
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| diff -r 000000000000 -r 4cb6c83d3777 test-data/pixel_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_out2.tabular Tue Feb 22 20:51:09 2022 +0000 |
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| @@ -0,0 +1,10 @@ +spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz annotation +xy_1_1 1 1 1 3672 11 42479 43 1267.525390625 col1 +xy_2_1 2 1 2 3672 8 29179 20 1264.42407226562 col2 +xy_3_1 3 1 3 3672 9 37005 42 1267.525390625 col3 +xy_1_2 1 2 4 3672 11 42306 49 1264.38171386719 col1 +xy_2_2 2 2 5 3672 8 30350 21 1267.525390625 col2 +xy_3_2 3 2 6 3672 9 35955 39 1199.55615234375 col3 +xy_1_3 1 3 7 3672 11 43872 84 1199.59753417969 col1 +xy_2_3 2 3 8 3672 9 33204 26 1267.48278808594 col2 +xy_3_3 3 3 9 3672 10 37961 47 1199.55615234375 col3 |
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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/probability_r2_k10_mz1135.93347167969.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/probability_r2_k10_mz1135.93347167969.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| b'@@ -0,0 +1,401 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|
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/random_factors.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_factors.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,24 @@ +1 1 f1 A +2 1 f1 A +3 1 f2 B +4 1 f1 C +1 2 f2 C +2 2 f2 C +3 2 f2 B +4 2 f2 A +1 3 f2 A +2 3 f1 B +3 3 f2 C +4 3 f1 A +10 1 f1 A +11 1 f2 C +12 1 f1 B +13 1 f1 B +10 2 f1 B +11 2 f1 A +12 2 f2 C +13 2 f2 A +10 3 f1 C +11 3 f2 B +12 3 f1 B +13 3 f2 C |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/rdata_notfiltered.pdf |
| b |
| Binary file test-data/rdata_notfiltered.pdf has changed |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/scores_pca.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_pca.tabular Tue Feb 22 20:51:09 2022 +0000 |
| b |
| @@ -0,0 +1,10 @@ +pixel names x y PC1 PC2 +xy_1_1 1 1 1.009701 0.757987 +xy_2_1 2 1 0.579669 -0.365615 +xy_3_1 3 1 -1.047904 0.831141 +xy_1_2 1 2 3.500409 0.608579 +xy_2_2 2 2 -0.325051 0.275855 +xy_3_2 3 2 -1.31375 0.01927 +xy_1_3 1 3 -1.461938 -0.033735 +xy_2_3 2 3 -1.088331 1.164611 +xy_3_3 3 3 0.147195 -3.258092 |
| b |
| diff -r 000000000000 -r 4cb6c83d3777 test-data/sd_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sd_out2.tabular Tue Feb 22 20:51:09 2022 +0000 |
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| diff -r 000000000000 -r 4cb6c83d3777 test-data/toplabels_proc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_proc.tabular Tue Feb 22 20:51:09 2022 +0000 |
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