| Next changeset 1:4257fc095049 (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:
colocalization.xml macros.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 d3ca64dafdef colocalization.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/colocalization.xml Tue Feb 22 20:52:51 2022 +0000 |
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| b'@@ -0,0 +1,222 @@\n+<tool id="cardinal_colocalization" name="MSI colocalization" version="@VERSION@.0">\n+ <description>mass spectrometry imaging colocalization</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 \'${MSI_colocalization}\' &&\n+ Rscript \'${MSI_colocalization}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_colocalization"><![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($reference_type.reference) == "roi_ref":\n+ ## read and extract x,y,annotation information\n+ input_tabular <- read.delim("$reference_type.annotation_file", header = $reference_type.tabular_header, stringsAsFactors = FALSE)\n+ annotation_input <- input_tabular[,c($reference_type.column_x, $reference_type.column_y, $reference_type.column_names)]\n+ annotation_name <- colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name\n+ colnames(annotation_input) <- c("x", "y", "annotation") ## rename annotations header to default name "annotation"\n+\n+ ## merge with coordinate information of msidata\n+ msidata_coordinates <- data.frame(coord(msidata)\\$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+ reference_group <- msidata\\$annotation == "$reference_type.ref_name"\n+#end if\n+\n+## remove duplicated coordinates\n+msidata <- msidata[,!duplicated(coord(msidata))]\n+\n+\n+@DATA_PROPERTIES_INRAM@\n+\n+\n+######################################## PDF ###################################\n+################################################################################\n+################################################################################\n+\n+\n+pdf("colocalization.pdf", fonts = "Times", pointsize = 12)\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n+\n+title(main=paste0("Colocalization for file: \\n\\n", "$infile.display_name"))\n+\n+grid.table(property_df, rows= NULL)\n+\n+\n+if (npeaks > 0 && sum(is.na(spectra(msidata)))==0)\n+{\n+\n+ ## colocalization analysis\n+ col_results <- colocalized(msidata, \n+ #if str($reference_type.reference) == "mz_ref":\n+ mz = $reference_type.mz_value,\n+ #else\n+ ref = reference_group,\n+ #end if\n+ n = $n_tophits,\n+ sort.by = "$sort_by",\n+ threshold = median)\n+\n+ ## Summary results table\n+ col_results_df <- as.data.frame(col_results)\n+\n+ write.table(col_results_df, file="$coloc_results", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\\t")\n+ \n+ ## visualize top 10 m/z features\n+\n+ if (nrow(col_results_df) <= 10)\n+ {\n+ for (mass in col_results_df\\$mz){\n+\t par(oma=c(0,0,0,1))## margin for image legend\n+\t print(image(msidata, mz=mass, plusminus=0.25,\n+\t main= paste0(round(mass, digits = 2)),\n+\t contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))\n+ }\n+ }else{\n+\tfor (mass in col_results_df\\$mz[1:10]){\n+\t par(oma=c(0,0,0,1))## margin for image legend\n+\t print(image(msidata, mz=mass, plusminus=0.25,\n+\t main= paste0(round(mass, digits = 2)),\n+\t contrast.enhance = "histogram", strip=FALSE, ylim= c(maximumy,minimumy)))\n+\t} \n+ }\n+ \n+\n+ dev.off()\n+ \n+}else{\n+ print("Inputfile has no intensities > 0")\n+}\n+\n+ ]]></confi'..b' <option value="M2">Manders\' colocalization coefficient 2</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data format="pdf" name="coloc_pdf" from_work_dir="colocalization.pdf" label = "${tool.name} on ${on_string}: results"/>\n+ <data format="tabular" name="coloc_results" label="${tool.name} on ${on_string}: summary"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+\t <param name="infile" value="" ftype="imzml">\n+\t <composite_data value="spatial_DGMM_input.imzML"/>\n+\t <composite_data value="spatial_DGMM_input.ibd"/>\n+\t </param>\n+\t <conditional name="reference_type">\n+\t <param name="reference" value="mz_ref"/>\n+\t <param name="mz_value" value="1000"/>\n+\t </conditional>\n+\t <output name="coloc_pdf" file="coloc1.pdf" compare="sim_size" delta="2000"/>\n+ <output name="coloc_results" file="coloc_table1.tabular"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="spatial_DGMM_input.imzML"/>\n+ <composite_data value="spatial_DGMM_input.ibd"/>\n+ </param>\n+\t<conditional name="reference_type">\n+ <param name="reference" value="roi_ref"/>\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+ <param name="ref_name" value="circle"/> \n+ </conditional>\n+ <param name="n_tophits" value="5"/>\n+ <param name="sort_by" value="M2"/>\n+\t <output name="coloc_pdf" file="coloc2.pdf" compare="sim_size" delta="2000"/>\n+ <output name="coloc_results" file="coloc_table2.tabular"/>\n+ </test>\n+ <test>\n+\t <param name="infile" value="123_combined.RData" ftype="rdata"/>\n+\t <conditional name="reference_type">\n+\t <param name="reference" value="mz_ref"/>\n+\t <param name="mz_value" value="102.0"/>\n+\t </conditional> \n+\t <param name="n_tophits" value="50"/>\n+\t <param name="sort_by" value="correlation"/>\n+\t <output name="coloc_pdf" file="coloc3.pdf" compare="sim_size" delta="2000"/>\n+\t <output name="coloc_results" file="coloc_table3.tabular"/>\n+ </test> \n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool finds colocalized features in an imaging dataset. Use it to find m/z features that are colocalized with another m/z feature or regions of interests. \n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+\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 and optionally filtered for m/z of interest in order to keep computational times reasonable.\n+\n+\n+**Options**\n+\n+- The reference can be either a single m/z feature or a region of interest provided via the annotation file. \n+\n+\t- For single m/z features the closest m/z to the m/z value that is used as reference is used\n+\t- For regions of interest as a reference the name of the region that should be used as a reference has to be written exactly in the way in which it appears in the annotation file input. \n+\t @SPECTRA_TABULAR_INPUT_DESCRIPTION@\n+\t\n+- By default, pearson correlation is used to rank the colocalized features. Manders\xe2\x80\x99 colocalization coefficients (M1 and M2) are also provided.\n+\n+**Output**\n+\n+- Pdf with file info and the ion images of the top 10 m/z features (to plot the ion images for more m/z features use the MSI mz images tool)\n+- Tabular file with the top m/z features and their correlation values (pearson, Manders 1 and Manders 2) with the reference\n+\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r d3ca64dafdef macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Feb 22 20:52:51 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 d3ca64dafdef 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 20:52:51 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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| @@ -0,0 +1,11 @@ +mz correlation M1 M2 +1023.70806884766 1 1 1 +1135.93347167969 0.94302593356566 0.875 0.875 +1200.46533203125 0.929209321928257 0.865 0.865 +1361.26818847656 0.671211137378556 0.71 0.71 +1227.93798828125 0.667168853181017 0.675 0.675 +1453.50952148438 0.665731065791311 0.695 0.695 +1858.89855957031 0.662094302798731 0.705 0.705 +781.236755371094 0.389123692250897 0.65 0.65 +473.920562744141 0.363240913030914 0.6 0.6 +788.86328125 0.337801573243261 0.605 0.605 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/coloc_table2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coloc_table2.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +mz correlation M1 M2 +473.920562744141 0.894244530237853 1 0.455 +788.86328125 0.767668409422198 1 0.455 +781.236755371094 0.702693174822292 0.989010989010989 0.45 +1135.93347167969 0.41173637823825 0.846153846153846 0.385 +1023.70806884766 0.332982169243747 0.791208791208791 0.36 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/coloc_table3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coloc_table3.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,51 @@ +mz correlation M1 M2 +100.583335876465 1 1 1 +100.666664123535 1 1 1 +100.75 1 1 1 +101.416664123535 1 1 1 +101.916664123535 1 1 1 +102 1 1 1 +102.416664123535 1 1 1 +103 1 1 1 +103.083335876465 1 1 1 +103.5 1 1 1 +103.583335876465 1 1 1 +104.083335876465 1 1 1 +104.583335876465 1 1 1 +104.666664123535 1 1 1 +105.166664123535 1 1 1 +113.5 1 1 0.4 +114.583335876465 1 1 0.666666666666667 +114.666664123535 1 1 0.666666666666667 +119.166664123535 1 1 1 +121.666664123535 1 1 1 +122.166664123535 1 1 1 +122.25 1 1 1 +127.083335876465 1 1 0.666666666666667 +127.166664123535 1 1 0.333333333333333 +127.25 1 1 0.333333333333333 +127.333335876465 1 1 0.4 +127.666664123535 1 1 0.666666666666667 +127.75 1 1 0.333333333333333 +128.25 1 1 0.333333333333333 +128.33332824707 1 1 0.333333333333333 +128.41667175293 1 1 0.4 +134.91667175293 1 1 0.5 +135.58332824707 1 1 0.5 +136.08332824707 1 1 0.5 +138.5 1 1 0.666666666666667 +166.33332824707 1 1 0.4 +166.83332824707 1 1 0.666666666666667 +166.91667175293 1 1 0.5 +167.41667175293 1 1 0.666666666666667 +167.83332824707 1 1 0.333333333333333 +167.91667175293 1 1 0.666666666666667 +168 1 1 1 +168.08332824707 1 1 1 +168.41667175293 1 1 0.5 +168.5 1 1 0.666666666666667 +168.58332824707 1 1 1 +169 1 1 0.666666666666667 +169.08332824707 1 1 1 +169.16667175293 1 1 1 +169.58332824707 1 1 0.666666666666667 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/dgmm_summary1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dgmm_summary1.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +r k Classes/group m/z Feature +1 6 2 473.920562744141 1 +1 6 4 781.236755371094 2 +1 6 1 788.86328125 3 +1 6 3 1023.70806884766 4 +1 6 3 1135.93347167969 5 +1 6 4 1200.46533203125 6 +1 6 2 1227.93798828125 7 +1 6 2 1361.26818847656 8 +1 6 2 1453.50952148438 9 +1 6 2 1858.89855957031 10 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/dgmm_summary2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dgmm_summary2.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +r k Classes/group m/z Feature +2 10 1 473.920562744141 1 +2 10 2 781.236755371094 2 +2 10 1 788.86328125 3 +2 10 1.67 1023.70806884766 4 +2 10 1.67 1135.93347167969 5 +2 10 1.67 1200.46533203125 6 +2 10 1 1227.93798828125 7 +2 10 1.67 1361.26818847656 8 +2 10 1 1453.50952148438 9 +2 10 1.33 1858.89855957031 10 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/dgmm_test1.pdf |
| b |
| Binary file test-data/dgmm_test1.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/dgmm_test2.RData |
| b |
| Binary file test-data/dgmm_test2.RData has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/dgmm_test2.pdf |
| b |
| Binary file test-data/dgmm_test2.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/empty_spectra.rdata |
| b |
| Binary file test-data/empty_spectra.rdata has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/estimates_r1_k6_mz1135.93347167969.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimates_r1_k6_mz1135.93347167969.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +group class mean var +files_ 1 0.172268980321456 0.133976695047921 +files_ 2 4.88607208725277 0.301220362077463 +files_ 3 6.64940193494161 0.752878508867188 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/estimates_r2_k10_mz1200.46533203125.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimates_r2_k10_mz1200.46533203125.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +group class mean var +bg 1 0.216553505243044 0.158967083338173 +bg 2 4.13395686852547 0.859771560896229 +circle 3 3.16694802842791 0.372813860593546 +circle 4 4.48944198265987 1.71739690046886 +square 5 3.8928901507304 1.21620428871296 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/features_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_out1.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,1200 @@\n+mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n+mz_300.083343505859\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n+mz_300.166687011719\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n+mz_300.25\t300.25\t1.77280128848483e-10\t0\t5.31840386545449e-10\t300\t1.59552115963635e-09\t1\n+mz_300.333343505859\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n+mz_300.416687011719\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n+mz_300.5\t300.5\t5.50704215937811e-06\t0\t1.65211264781343e-05\t300\t4.9563379434403e-05\t1\n+mz_300.583343505859\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n+mz_300.666687011719\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n+mz_300.75\t300.75\t1.30250899042089e-14\t0\t3.90752697126268e-14\t300\t1.1722580913788e-13\t1\n+mz_300.833343505859\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n+mz_300.916687011719\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n+mz_301\t301\t0\t0\t0\tNA\t0\t0\n+mz_301.083343505859\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n+mz_301.166687011719\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n+mz_301.25\t301.25\t1.04927193477088e-11\t0\t3.14781580431263e-11\t300\t9.4434474129379e-11\t1\n+mz_301.333343505859\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n+mz_301.416687011719\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n+mz_301.5\t301.5\t1.36295095239794e-20\t0\t4.08885285719383e-20\t300\t1.22665585715815e-19\t1\n+mz_301.583343505859\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n+mz_301.666687011719\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n+mz_301.75\t301.75\t2.98124144276739e-15\t0\t8.94372432830217e-15\t300\t2.68311729849065e-14\t1\n+mz_301.833343505859\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n+mz_301.916687011719\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n+mz_302\t302\t4.80219917504923e-24\t0\t1.44065975251477e-23\t300\t4.32197925754431e-23\t1\n+mz_302.083343505859\t302.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_302.166687011719\t302.166687011719\t1.99229097511357e-18\t0\t5.97687292534071e-18\t300\t1.79306187760221e-17\t1\n+mz_302.25\t302.25\t5.44512547500737e-19\t0\t1.63353764250221e-18\t300\t4.90061292750663e-18\t1\n+mz_302.333343505859\t302.333343505859\t3.63632770555763e-20\t0\t1.09089828246395e-19\t299.999991969003\t3.27269493500187e-19\t2\n+mz_302.416687011719\t302.416687011719\t3.84359191432166e-27\t0\t1.1530775742965e-26\t300\t3.45923272288949e-26\t1\n+mz_302.5\t302.5\t9.40271183279141e-28\t0\t2.82081354983742e-27\t300\t8.46244064951227e-27\t1\n+mz_302.583343505859\t302.583343505859\t4.19068660396836e-29\t0\t1.25720598119051e-28\t300\t3.77161794357152e-28\t1\n+mz_302.666687011719\t302.666687011719\t0.00150662205285496\t0\t0.00451986615856489\t300\t0.0135595984756947\t2\n+mz_302.75\t302.75\t0.0266792873541514\t0\t0.0800378620624542\t300\t0.240113586187363\t2\n+mz_302.833343505859\t302.833343505859\t0.0301816893948449\t0\t0.0905450681845347\t300\t0.271635204553604\t2\n+mz_302.916687011719\t302.916687011719\t0.0074387863278389\t0\t0.0223163589835167\t300\t0.0669490769505501\t2\n+mz_303\t303\t0.000343241521881686\t0\t0.00102972456564506\t300\t0.00308917369693518\t2\n+mz_303.083343505859\t303.083343505859\t1.90888501507935e-32\t0\t5.72665504523804e-32\t300\t1.71799651357141e-31\t1\n+mz_303.166687011719\t303.166687011719\t9.50172003937247e-28\t0\t2.85051601181174e-27\t300\t8.55154803543523e-27\t1\n+mz_303.25\t303.25\t9.25846532935131e-27\t0\t2.77753959880539e-26\t300\t8.33261879641618e-26\t1\n+mz_303.333343505859\t303.333343505859\t2.64138078718032e-06\t0\t7.92414236154097'..b'05859\t1.28880310833658e-06\t0\t3.86640931417449e-06\t299.999999159279\t1.15992279750292e-05\t2\n+mz_396.666687011719\t396.666687011719\t1.19932843361377e-07\t0\t3.5979852924763e-07\t299.999999302525\t1.0793955902524e-06\t2\n+mz_396.75\t396.75\t9.85288224826943e-15\t0\t2.95586467448083e-14\t300\t8.86759402344249e-14\t1\n+mz_396.833343505859\t396.833343505859\t4.96342371199506e-15\t0\t1.48902711359651e-14\t299.999999999595\t4.46708134079555e-14\t3\n+mz_396.916687011719\t396.916687011719\t7.61762987489752e-16\t0\t2.2852889624605e-15\t299.99999999885\t6.85586688740777e-15\t3\n+mz_397\t397\t0.00431232982211643\t0\t0.0129369894663493\t300\t0.0388109683990479\t3\n+mz_397.083343505859\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 d3ca64dafdef test-data/features_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_out3.tabular Tue Feb 22 20:52:51 2022 +0000 |
| 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 d3ca64dafdef test-data/features_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_out4.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,10399 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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/features_test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test2.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/features_test4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test4.tabular Tue Feb 22 20:52:51 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/features_test6.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test6.tabular Tue Feb 22 20:52:51 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/features_test7.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_test7.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/featuresofinterest5.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featuresofinterest5.tabular Tue Feb 22 20:52:51 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 d3ca64dafdef test-data/imzml_filtered3.pdf |
| b |
| Binary file test-data/imzml_filtered3.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/imzml_filtered4.pdf |
| b |
| Binary file test-data/imzml_filtered4.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/imzml_filtered5.pdf |
| b |
| Binary file test-data/imzml_filtered5.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/imzml_filtered8.pdf |
| b |
| Binary file test-data/imzml_filtered8.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/inputcalibrantfile1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile1.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +101.5 +356.7 +555.1 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/inputcalibrantfile2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile2.txt Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +869.51 mass1 +1111.1 mass2 +1296.7 mass3 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/inputpeptides.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +152 mass1 +328.9 mass2 +185.2 mass3 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/inputpeptides2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpeptides2.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +854.5 +1111.1 +1296.7 +1305.1 |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/inputpixels_2column.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels_2column.tabular Tue Feb 22 20:52:51 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 d3ca64dafdef test-data/int_matrix1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_matrix1.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,1200 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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/int_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_matrix3.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,1200 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| diff -r 000000000000 -r d3ca64dafdef test-data/kmeans_analyze.pdf |
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| Binary file test-data/kmeans_analyze.pdf has changed |
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| diff -r 000000000000 -r d3ca64dafdef test-data/mean_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mean_out2.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/picked.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picked.imzml.txt Tue Feb 22 20:52:51 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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| diff -r 000000000000 -r d3ca64dafdef test-data/picked.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picked.tabular Tue Feb 22 20:52:51 2022 +0000 |
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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 d3ca64dafdef test-data/picked_QC.pdf |
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| Binary file test-data/picked_QC.pdf has changed |
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| diff -r 000000000000 -r d3ca64dafdef test-data/pixel_annotation_file1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_annotation_file1.tabular Tue Feb 22 20:52:51 2022 +0000 |
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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 d3ca64dafdef test-data/pixel_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_out2.tabular Tue Feb 22 20:52:51 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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| diff -r 000000000000 -r d3ca64dafdef test-data/pixel_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_out3.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/pixel_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_out4.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/pixels_test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixels_test2.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/pixels_test4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixels_test4.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| @@ -0,0 +1,25 @@ +pixel names x y predicted condition +xy_1_1 1 1 A +xy_2_1 2 1 C +xy_3_1 3 1 B +xy_4_1 4 1 C +xy_1_2 1 2 C +xy_2_2 2 2 C +xy_3_2 3 2 B +xy_4_2 4 2 A +xy_1_3 1 3 A +xy_2_3 2 3 B +xy_3_3 3 3 C +xy_4_3 4 3 A +xy_10_1 10 1 A +xy_11_1 11 1 C +xy_12_1 12 1 C +xy_13_1 13 1 B +xy_10_2 10 2 B +xy_11_2 11 2 A +xy_12_2 12 2 C +xy_13_2 13 2 A +xy_10_3 10 3 C +xy_11_3 11 3 B +xy_12_3 12 3 B +xy_13_3 13 3 C |
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| diff -r 000000000000 -r d3ca64dafdef test-data/pixels_test7.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixels_test7.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| @@ -0,0 +1,25 @@ +pixel names x y predicted condition +xy_1_1 1 1 A +xy_2_1 2 1 A +xy_3_1 3 1 A +xy_4_1 4 1 A +xy_1_2 1 2 B +xy_2_2 2 2 B +xy_3_2 3 2 B +xy_4_2 4 2 B +xy_1_3 1 3 C +xy_2_3 2 3 C +xy_3_3 3 3 C +xy_4_3 4 3 C +xy_10_1 10 1 A +xy_11_1 11 1 A +xy_12_1 12 1 A +xy_13_1 13 1 A +xy_10_2 10 2 B +xy_11_2 11 2 B +xy_12_2 12 2 B +xy_13_2 13 2 B +xy_10_3 10 3 B +xy_11_3 11 3 C +xy_12_3 12 3 C +xy_13_3 13 3 C |
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| diff -r 000000000000 -r d3ca64dafdef test-data/preprocessing_results1.ibd |
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| diff -r 000000000000 -r d3ca64dafdef test-data/preprocessing_results5.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results5.imzml.txt Tue Feb 22 20:52:51 2022 +0000 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 428 +-rw-rw-r-- 1 meli meli 415936 Oct 5 19:59 ibd +-rw-rw-r-- 1 meli meli 18569 Oct 5 19:59 imzml |
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| diff -r 000000000000 -r d3ca64dafdef test-data/preprocessing_results5.pdf |
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| Binary file test-data/preprocessing_results5.pdf has changed |
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| diff -r 000000000000 -r d3ca64dafdef test-data/probability_r1_k6_mz1023.70806884766.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/probability_r1_k6_mz1023.70806884766.tabular Tue Feb 22 20:52:51 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r d3ca64dafdef 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 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,401 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|
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/random_factors.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_factors.tabular Tue Feb 22 20:52:51 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 d3ca64dafdef test-data/rdata_notfiltered.pdf |
| b |
| Binary file test-data/rdata_notfiltered.pdf has changed |
| b |
| diff -r 000000000000 -r d3ca64dafdef test-data/scores_pca.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_pca.tabular Tue Feb 22 20:52:51 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 d3ca64dafdef test-data/sd_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sd_out2.tabular Tue Feb 22 20:52:51 2022 +0000 |
| b |
| b'@@ -0,0 +1,3673 @@\n+mz 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| diff -r 000000000000 -r d3ca64dafdef test-data/spatial_DGMM_input.ibd |
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| Binary file test-data/spatial_DGMM_input.ibd has changed |
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| diff -r 000000000000 -r d3ca64dafdef test-data/spatial_DGMM_input.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spatial_DGMM_input.imzML Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/spectra_1_pixel.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectra_1_pixel.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/spectra_info_imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectra_info_imzml.txt Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/tabular_LM8file16.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_LM8file16.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| @@ -0,0 +1,2 @@ +inputmz countpixels percentpixels +1111.1 0 0 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/tabular_analyze75.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_analyze75.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| @@ -0,0 +1,3 @@ +inputmz countpixels percentpixels +1296.7 9 100 +1305.1 9 100 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/tabular_imzml.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_imzml.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/toplabels_proc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_proc.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/toplabels_skm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_skm.tabular Tue Feb 22 20:52:51 2022 +0000 |
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| diff -r 000000000000 -r d3ca64dafdef test-data/toplabels_ssc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_ssc.tabular Tue Feb 22 20:52:51 2022 +0000 |
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