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Changeset 0:28ba52c9548c (2018-10-01)

Next changeset 1:65ef413a35f3 (2018-10-25)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415

added:
data_exporter.xml
macros.xml
test-data/112_annotation_output.tabular
test-data/112_auto_combined.RData
test-data/112_auto_combined_QC.pdf
test-data/123_annotation.tabular
test-data/123_annotation_output.tabular
test-data/123_combined.RData
test-data/123_combined_QC.pdf
test-data/12_annotation_output.tabular
test-data/12_combined.RData
test-data/12_combined_QC.pdf
test-data/2123_annotation_output.tabular
test-data/2123_auto_combined.RData
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/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_rdata.pdf
test-data/Plot_analyze75.pdf
test-data/Plot_analyze75_allpixels.pdf
test-data/Plot_empty_spectra.pdf
test-data/Plot_imzml.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_rdata.pdf
test-data/analyze75.svg
test-data/analyze75_filtered2.pdf
test-data/analyze_filtered.RData
test-data/analyze_filtered.pdf
test-data/analyze_filteredoutside.RData
test-data/analyze_originaloutput.RData
test-data/analyze_originaloutput2.RData
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_rdata.pdf
test-data/classes_ssc.tabular
test-data/cluster_skm.RData
test-data/cluster_skm.tabular
test-data/empty_spectra.rdata
test-data/features_out1.tabular
test-data/features_out3.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_filtered.RData
test-data/imzml_filtered.pdf
test-data/imzml_filtered2.RData
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/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/loadings_pca.tabular
test-data/mean_out2.tabular
test-data/msidata_1.RData
test-data/msidata_2.RData
test-data/msidata_3.RData
test-data/pca_imzml.pdf
test-data/pixel_annotation_file1.tabular
test-data/pixel_out2.tabular
test-data/pixel_out3.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/preprocessed.rdata
test-data/preprocessing_results1.RData
test-data/preprocessing_results1.pdf
test-data/preprocessing_results1.txt
test-data/preprocessing_results2.RData
test-data/preprocessing_results2.pdf
test-data/preprocessing_results2.txt
test-data/preprocessing_results3.RData
test-data/preprocessing_results3.pdf
test-data/preprocessing_results4.RData
test-data/preprocessing_results4.pdf
test-data/preprocessing_results4.txt
test-data/preprocessing_results5.RData
test-data/preprocessing_results5.pdf
test-data/preprocessing_results5.txt
test-data/random_factors.tabular
test-data/rdata_notfiltered.RData
test-data/rdata_notfiltered.pdf
test-data/scores_pca.tabular
test-data/sd_out2.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_skm.tabular
test-data/toplabels_ssc.tabular
test-data/xy_coordinates.tabular

diff -r 000000000000 -r 28ba52c9548c data_exporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_exporter.xml Mon Oct 01 01:05:33 2018 -0400

[

b'@@ -0,0 +1,359 @@\n+<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">\n+ <description>\n+ exports imzML and Analyze7.5 to tabular files\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ @INPUT_LINKING@\n+ cat \'${cardinal_imzml_exporter}\' &&\n+ Rscript \'${cardinal_imzml_exporter}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="cardinal_imzml_exporter"><![CDATA[\n+\n+################################# load libraries and read file #################\n+\n+library(Cardinal)\n+\n+@READING_MSIDATA@\n+\n+npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)\n+\n+if (npeaks > 0){\n+\n+ ###################### Intensity matrix output ################################\n+\n+ #if "int_matrix" in str($output_options).split(","):\n+ print("intensity matrix output")\n+\n+ spectramatrix = spectra(msidata)[]\n+ mz_names = gsub(" = ", "_", names(features(msidata)))\n+ mz_names = gsub("/", "", mz_names)\n+ pixel_names = gsub(", y = ", "_", names(pixels(msidata)))\n+ pixel_names = gsub(" = ", "y_", pixel_names)\n+\n+ spectramatrix = cbind(mz_names,spectramatrix)\n+ newmatrix = rbind(c("mz_name", pixel_names), spectramatrix)\n+ write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\\t")\n+\n+ #end if\n+\n+\n+ ############################## m/z feature output ##########################\n+ #if "mz_tabular" in str($output_options).split(","):\n+ print("mz feature output")\n+\n+ mz_names = gsub(" = ", "_", names(features(msidata)))\n+ mz_names = gsub("/", "", mz_names)\n+\n+ ## mean, median, sd and SEM intensity per file and mz\n+ full_sample_mean = apply(spectra(msidata)[],1,mean, na.rm=TRUE)\n+ full_sample_median = apply(spectra(msidata)[],1,median, na.rm=TRUE)\n+ full_sample_sd = apply(spectra(msidata)[],1,sd, na.rm=TRUE)\n+ full_sample_sem = full_sample_sd/full_sample_mean*100\n+ ## npeaks and sum of all intensities per spectrum and mz\n+ mzTIC = rowSums(spectra(msidata)[], na.rm=TRUE) ## calculate intensity sum for each m/z\n+ peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra)\n+\n+ ## combine into dataframe, order is the same for all vectors\n+ mz_df = data.frame(mz_names, mz(msidata), full_sample_mean, full_sample_median, full_sample_sd, full_sample_sem, mzTIC, peakspermz)\n+ colnames(mz_df) = c("mz_names", "mz", "sample_mean", "sample_median", "sample_sd", "sample_sem", "intensity_sum", "number_peaks")\n+ write.table(mz_df, file="$feature_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\\t")\n+ #end if\n+\n+ ###################### summarized m/z feature output #######################\n+\n+ #if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n+ print("summarized annotation output")\n+\n+ ## read and extract x,y,annotation information\n+ input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)\n+ annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]\n+ colnames(annotation_input) = c("x", "y", "annotation")\n+\n+ ## merge with coordinate information of msidata\n+ msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))\n+ colnames(msidata_coordinates)[3] = "pixel_index"\n+ merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)\n+ merged_annotation[is.na(merged_annotation)] = "NA"\n+ merged_annotation = merged_annotation[order(merged_annotation\\$pixel_index),]\n+ msidata\\$ann'..b' <filter>"mz_tabular" in output_options</filter>\n+ </data>\n+ <data format="tabular" name="summarized_mean" label="${tool.name} on ${on_string}: group_mean">\n+ <filter>tabular_annotation[\'load_annotation\'] == \'yes_annotation\' and \'mean\' in tabular_annotation[\'summary_type\']</filter>\n+ </data>\n+ <data format="tabular" name="summarized_median" label="${tool.name} on ${on_string}: group_median">\n+ <filter>tabular_annotation[\'load_annotation\'] == \'yes_annotation\' and \'median\' in tabular_annotation[\'summary_type\']</filter>\n+ </data>\n+ <data format="tabular" name="summarized_sd" label="${tool.name} on ${on_string}: group_sd">\n+ <filter>tabular_annotation[\'load_annotation\'] == \'yes_annotation\' and \'sd\' in tabular_annotation[\'summary_type\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="2">\n+ <expand macro="infile_imzml"/>\n+ <param name="output_options" value="int_matrix,mz_tabular"/>\n+ <output name="intensity_matrix" file="int_matrix1.tabular"/>\n+ <output name="feature_output" file="features_out1.tabular"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <expand macro="infile_analyze75"/>\n+ <param name="output_options" value="pixel_tabular"/>\n+ <conditional name="tabular_annotation">\n+ <param name="load_annotation" value="yes_annotation"/>\n+ <param name="annotation_file" value="annotations.tabular"/>\n+ <param name="column_x" value="1"/>\n+ <param name="column_y" value="2"/>\n+ <param name="column_names" value="4"/>\n+ <param name="tabular_header" value="True"/>\n+ <param name="summary_type" value="mean,sd"/>\n+ </conditional>\n+ <output name="pixel_output" file="pixel_out2.tabular"/>\n+ <output name="summarized_mean" file="mean_out2.tabular"/>\n+ <output name="summarized_sd" file="sd_out2.tabular"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <expand macro="infile_imzml"/>\n+ <param name="output_options" value="int_matrix,pixel_tabular,mz_tabular"/>\n+ <conditional name="counting_calibrants">\n+ <param name="pixel_with_calibrants" value="yes_calibrants"/>\n+ <param name="mz_tabular" value="inputcalibrantfile2.txt"/>\n+ <param name="feature_column" value="1"/>\n+ <param name="feature_header" value="False"/>\n+ <param name="plusminus_ppm" value="200"/>\n+ </conditional>\n+ <output name="intensity_matrix" file="int_matrix3.tabular"/>\n+ <output name="feature_output" file="features_out3.tabular"/>\n+ <output name="pixel_output" file="pixel_out3.tabular"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool provides multiple tabular output options for mass spectrometry imaging data files. \n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+\n+@SPECTRA_TABULAR_INPUT_DESCRIPTION@\n+\n+@MZ_TABULAR_INPUT_DESCRIPTION@\n+\n+**Output options**\n+\n+- intensity matrix: m/z in rows, spectra in columns, filled with intensity values\n+- spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), highest m/z feature per spectrum, optional count of input m/z per spectrum, optional spectrum annotation\n+- mz feature output: m/z in rows - for each m/z: name, m/z, mean, median, standard deviation (sd), standard error of the mean (sem), sum of all intensities per m/z, number of peaks (intensity > 0) per m/z\n+- summarized intensities: pixel annotations will be used to group spectra into annotation groups and calculate mean, median and sd of the intensities per group\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 28ba52c9548c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 01 01:05:33 2018 -0400

[

b'@@ -0,0 +1,236 @@\n+<macros>\r\n+ <token name="@VERSION@">1.12.1</token>\r\n+\r\n+ <xml name="requirements">\r\n+ <requirements>\r\n+ <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>\r\n+ <yield/>\r\n+ </requirements>\r\n+ </xml>\r\n+\r\n+ <token name="@INPUT_LINKING@"><![CDATA[\r\n+ #if $infile.ext == \'imzml\'\r\n+ ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\r\n+ ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\r\n+ #elif $infile.ext == \'analyze75\'\r\n+ ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\r\n+ ln -s \'${infile.extra_files_path}/img\' infile.img &&\r\n+ ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\r\n+ #else\r\n+ ln -s $infile infile.RData &&\r\n+ #end if\r\n+ ]]></token>\r\n+\r\n+\r\n+ <token name="@READING_MSIDATA@"><![CDATA[\r\n+ ## importing MSI data files\r\n+\r\n+ ## function to read RData files independent of filename\r\n+ loadRData <- function(fileName){\r\n+ load(fileName)\r\n+ get(ls()[ls() != "fileName"])\r\n+ }\r\n+\r\n+ #if $infile.ext == \'imzml\'\r\n+ #if str($processed_cond.processed_file) == "processed":\r\n+ msidata <- readImzML(\'infile\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")\r\n+ centroided(msidata) = $centroids\r\n+ #else\r\n+ msidata <- readImzML(\'infile\')\r\n+ centroided(msidata) = $centroids\r\n+ #end if\r\n+ #elif $infile.ext == \'analyze75\'\r\n+ msidata = readAnalyze(\'infile\')\r\n+ centroided(msidata) = $centroids\r\n+ #else\r\n+ msidata = loadRData(\'infile.RData\')\r\n+ #end if\r\n+\r\n+ ]]></token>\r\n+\r\n+ <token name="@DATA_PROPERTIES@"><![CDATA[\r\n+ ## Number of features (mz)\r\n+ maxfeatures = length(features(msidata))\r\n+ ## Range mz\r\n+ minmz = round(min(mz(msidata)), digits=2)\r\n+ maxmz = round(max(mz(msidata)), digits=2)\r\n+ ## Number of spectra (pixels)\r\n+ pixelcount = length(pixels(msidata))\r\n+ ## Range x coordinates\r\n+ minimumx = min(coord(msidata)[,1])\r\n+ maximumx = max(coord(msidata)[,1])\r\n+ ## Range y coordinates\r\n+ minimumy = min(coord(msidata)[,2])\r\n+ maximumy = max(coord(msidata)[,2])\r\n+ ## Range of intensities\r\n+ minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)\r\n+ maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)\r\n+ ## Number of intensities > 0, for if conditions\r\n+ npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)\r\n+\r\n+ properties = c("Number of m/z features",\r\n+ "Range of m/z values",\r\n+ "Number of pixels", \r\n+ "Range of x coordinates", \r\n+ "Range of y coordinates",\r\n+ "Range of intensities")\r\n+\r\n+ values = c(paste0(maxfeatures), \r\n+ paste0(minmz, " - ", maxmz), \r\n+ paste0(pixelcount), \r\n+ paste0(minimumx, " - ", maximumx), \r\n+ paste0(minimumy, " - ", maximumy), \r\n+ paste0(minint, " - ", maxint))\r\n+\r\n+ property_df = data.frame(properties, values)\r\n+ ]]></token>\r\n+\r\n+ <token name="@CARDINAL_DESCRIPTION@"><![CDATA[\r\n+ Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets.\r\n+ `More information on Cardinal <http://cardinalmsi.org/>`_\r\n+ ]]></token>\r\n+ <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[\r\n+ **Input data**\r\n+\r\n+ - MSI data: 3 types of input data can be used:\r\n+\r\n+ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\r\n+ - Analyze7.5 (upload hd'..b'o_processed"/>\r\n+ <when value="processed">\r\n+ <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>\r\n+ <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">\r\n+ <option value="mz" >mz</option>\r\n+ <option value="ppm" selected="True" >ppm</option>\r\n+ </param>\r\n+ </when>\r\n+ </conditional>\r\n+ </xml>\r\n+\r\n+ <xml name="pdf_filename">\r\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">\r\n+ <sanitizer invalid_char="">\r\n+ <valid initial="string.ascii_letters,string.digits">\r\n+ <add value="_" />\r\n+ </valid>\r\n+ </sanitizer>\r\n+ </param>\r\n+ </xml>\r\n+\r\n+ <xml name="sanitizer_multiple_digits">\r\n+ <sanitizer invalid_char="">\r\n+ <valid initial="string.digits">\r\n+ <add value=":" />\r\n+ <add value="," />\r\n+ </valid>\r\n+ </sanitizer>\r\n+ </xml>\r\n+\r\n+ <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">\r\n+ <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>\r\n+ <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>\r\n+ <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\r\n+ </xml>\r\n+\r\n+ <xml name="reading_2_column_mz_tabular">\r\n+ <param name="calibrant_file" type="data" optional="true" format="tabular"\r\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)"/>\r\n+ <param name="mz_column" data_ref="calibrant_file" label="Column with m/z values" type="data_column"/>\r\n+ <param name="name_column" data_ref="calibrant_file" label="Column with name of m/z values" type="data_column"/>\r\n+ <param name="calibrant_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\r\n+ </xml>\r\n+\r\n+ <xml name="reading_pixel_annotations">\r\n+ <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"\r\n+ help="Tabular file with three columns: x values, y values and pixel annotations"/>\r\n+ <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>\r\n+ <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>\r\n+ <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>\r\n+ <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\r\n+ </xml>\r\n+\r\n+ <xml name="citations">\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\r\n+ </citations>\r\n+ </xml>\r\n+ <xml name="infile_analyze75">\r\n+ <param name="infile" value="" ftype="analyze75">\r\n+ <composite_data value="Analyze75.hdr"/>\r\n+ <composite_data value="Analyze75.img"/>\r\n+ <composite_data value="Analyze75.t2m"/>\r\n+ </param>\r\n+ </xml>\r\n+ <xml name="infile_imzml">\r\n+ <param name="infile" value="" ftype="imzml">\r\n+ <composite_data value="Example_Continuous.imzML"/>\r\n+ <composite_data value="Example_Continuous.ibd"/>\r\n+ </param>\r\n+ </xml>\r\n+</macros>\r\n'

diff -r 000000000000 -r 28ba52c9548c test-data/112_annotation_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_annotation_output.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,16 @@
+x y sample_name file_name column_name NA.x NA.y NA
+1 1 msidata_1.RData file_one col1 NA NA NA
+1 2 msidata_1.RData file_one col1 NA NA NA
+1 3 msidata_1.RData file_one col1 NA NA NA
+10 1 123_combined.RData file_two col3 NA NA NA
+10 2 123_combined.RData file_two col3 NA NA NA
+10 3 123_combined.RData file_two col3 NA NA NA
+15 1 123_combined.RData file_three col3 NA NA NA
+15 2 123_combined.RData file_three col3 NA NA NA
+15 3 123_combined.RData file_three col3 NA NA NA
+7 1 123_combined.RData file_one col1 NA NA NA
+7 2 123_combined.RData file_one col1 NA NA NA
+7 3 123_combined.RData file_one col1 NA NA NA
+9 1 123_combined.RData file_two col2 NA NA NA
+9 2 123_combined.RData file_two col2 NA NA NA
+9 3 123_combined.RData file_two col2 NA NA NA

diff -r 000000000000 -r 28ba52c9548c test-data/112_auto_combined.RData

Binary file test-data/112_auto_combined.RData has changed

diff -r 000000000000 -r 28ba52c9548c test-data/112_auto_combined_QC.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/123_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,13 @@
+x y file_name column_name
+1 1 file_one col1
+1 2 file_one col1
+1 3 file_one col1
+3 1 file_two col2
+3 2 file_two col2
+3 3 file_two col2
+4 1 file_two col3
+4 2 file_two col3
+4 3 file_two col3
+9 1 file_three col3
+9 2 file_three col3
+9 3 file_three col3

diff -r 000000000000 -r 28ba52c9548c test-data/123_annotation_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation_output.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,13 @@
+x y sample_name file_name column_name NA.x NA.y NA
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2711359651e-14\t299.999999999595\t4.46708134079555e-14\t3\n+mz_396.92\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_397.08\t397.083343505859\t0.032068928082784\t0\t0.0962067842483521\t300\t0.288620352745056\t2\n+mz_397.17\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_397.33\t397.333343505859\t5.81765407613358e-19\t0\t1.74529622283953e-18\t299.999999999906\t5.23588866852022e-18\t2\n+mz_397.42\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_397.58\t397.583343505859\t5.19108733658977e-23\t0\t1.55732620090041e-22\t299.99999998526\t4.67197860293079e-22\t2\n+mz_397.67\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_397.83\t397.833343505859\t5.05598304951289e-08\t0\t1.51679491485387e-07\t300\t4.5503847445616e-07\t2\n+mz_397.92\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_398.08\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n+mz_398.17\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_398.33\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n+mz_398.42\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_398.58\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n+mz_398.67\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_398.83\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n+mz_398.92\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n+mz_399\t399\t0\t0\t0\tNA\t0\t0\n+mz_399.08\t399.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.17\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_399.33\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n+mz_399.42\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_399.58\t399.583343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.67\t399.666687011719\t0\t0\t0\tNA\t0\t0\n+mz_399.75\t399.75\t0\t0\t0\tNA\t0\t0\n+mz_399.83\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n+mz_399.92\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n'

diff -r 000000000000 -r 28ba52c9548c test-data/features_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out3.tabular Mon Oct 01 01:05:33 2018 -0400

diff -r 000000000000 -r 28ba52c9548c test-data/features_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test2.tabular Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,101 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diff -r 000000000000 -r 28ba52c9548c test-data/features_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test4.tabular Mon Oct 01 01:05:33 2018 -0400

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diff -r 000000000000 -r 28ba52c9548c test-data/features_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test6.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,21 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/features_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test7.tabular Mon Oct 01 01:05:33 2018 -0400

diff -r 000000000000 -r 28ba52c9548c test-data/featuresofinterest5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:05:33 2018 -0400

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diff -r 000000000000 -r 28ba52c9548c test-data/imzml_filtered5.RData

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diff -r 000000000000 -r 28ba52c9548c test-data/inputcalibrantfile1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/inputcalibrantfile2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/inputpeptides.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/inputpeptides2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,4 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/inputpixels_2column.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,6 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/int_matrix1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix1.tabular Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 28ba52c9548c test-data/int_matrix3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix3.tabular Mon Oct 01 01:05:33 2018 -0400

diff -r 000000000000 -r 28ba52c9548c test-data/kmeans_analyze.pdf

Binary file test-data/kmeans_analyze.pdf has changed

diff -r 000000000000 -r 28ba52c9548c test-data/loadings_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loadings_pca.tabular Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 28ba52c9548c test-data/mean_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_out2.tabular Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,3673 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t6.33333333333333\t6.66666666666667\n+mz_1353\t9.66666666666667\t7.66666666666667\t8.66666666666667\n+mz_1353.05\t8.66666666666667\t7.33333333333333\t8.33333333333333\n+mz_1353.09\t8.33333333333333\t7.33333333333333\t9.66666666666667\n+mz_1353.13\t10.3333333333333\t9\t8\n+mz_1353.18\t9.66666666666667\t8.33333333333333\t7.66666666666667\n+mz_1353.22\t10.6666666666667\t7.66666666666667\t9\n+mz_1353.27\t8.66666666666667\t7.66666666666667\t9.66666666666667\n+mz_1353.31\t10.3333333333333\t8.33333333333333\t9\n+mz_1353.35\t11\t8\t7.66666666666667\n+mz_1353.4\t13.3333333333333\t8.33333333333333\t9\n+mz_1353.44\t14\t10.6666666666667\t11\n+mz_1353.48\t16\t9.66666666666667\t10.6666666666667\n+mz_1353.53\t16.3333333333333\t10.6666666666667\t13.3333333333333\n+mz_1353.57\t15\t11.6666666666667\t11.6666666666667\n+mz_1353.62\t12.3333333333333\t8.66666666666667\t12.3333333333333\n+mz_1353.66\t11.6666666666667\t10.3333333333333\t12\n+mz_1353.7\t12.3333333333333\t9.33333333333333\t11.3333333333333\n+mz_1353.75\t13.6666666666667\t7.66666666666667\t10.3333333333333\n+mz_1353.79\t11\t8.66666666666667\t9.33333333333333\n+mz_1353.84\t11\t7.33333333333333\t10\n+mz_1353.88\t10\t7.33333333333333\t8.66666666666667\n+mz_1353.92\t9.66666666666667\t6.66666666666667\t8\n+mz_1353.97\t10\t8.66666666666667\t9.33333333333333\n+mz_1354.01\t9.33333333333333\t8.66666666666667\t9.33333333333333\n+mz_1354.06\t9\t8.66666666666667\t7.33333333333333\n+mz_1354.1\t9\t7.33333333333333\t7.33333333333333\n+mz_1354.14\t9.66666666666667\t9.33333333333333\t8.33333333333333\n+mz_1354.19\t11\t9.66666666666667\t8\n+mz_1354.23\t10.6666666666667\t8\t9.66666666666667\n+mz_1354.28\t10.3333333333333\t8.66666666666667\t7.66666666666667\n+mz_1354.32\t11.3333333333333\t8.33333333333333\t8.66666666666667\n+mz_1354.36\t14\t8.66666666666667\t9\n+mz_1354.41\t17.6666666666667\t10\t14.3333333333333\n+mz_1354.45\t23.6666666666667\t12\t20.3333333333333\n+mz_1354.5\t21\t13.3333333333333\t21\n+mz_1354.54\t24\t14\t18.6666666666667\n+mz_1354.58\t19\t11.6666666666667\t16.6666666666667\n+mz_1354.63\t16.3333333333333\t11.3333333333333\t14\n+mz_1354.67\t16\t9\t13\n+mz_1354.72\t14.3333333333333\t8.66666666666667\t10.6666666666667\n+mz_1354.76\t15\t8\t11\n+mz_1354.8\t14.6666666666667\t8.33333333333333\t9.33333333333333\n+mz_1354.85\t10.6666666666667\t8.66666666666667\t10\n+mz_1354.89\t11\t8.66666666666667\t9\n+mz_1354.93\t9.66666666666667\t8.33333333333333\t10.6666666666667\n+mz_1354.98\t11.3333333333333\t8\t8\n+mz_1355.02\t9.33333333333333\t9\t9.66666666666667\n+mz_1355.07\t10.3333333333333\t6.66666666666667\t8.66666666666667\n+mz_1355.11\t8.66666666666667\t7\t9\n+mz_1355.15\t9.33333333333333\t7\t7.33333333333333\n+mz_1355.2\t10\t8\t8.66666666666667\n+mz_1355.24\t9.33333333333333\t8\t9.33333333333333\n+mz_1355.29\t11\t7.33333333333333\t9.33333333333333\n+mz_1355.33\t13\t8.33333333333333\t8.66666666666667\n+mz_1355.37\t12.6666666666667\t8\t11.6666666666667\n+mz_1355.42\t15.3333333333333\t8.66666666666667\t12.3333333333333\n+mz_1355.46\t18.3333333333333\t10.3333333333333\t12\n+mz_1355.51\t20.3333333333333\t9.33333333333333\t13.6666666666667\n+mz_1355.55\t19\t12\t15\n+mz_1355.59\t17\t10\t14.3333333333333\n+mz_1355.64\t15\t9.66666666666667\t12.6666666666667\n+mz_1355.68\t14.6666666666667\t9\t11\n+mz_1355.73\t13.3333333333333\t8\t13\n+mz_1355.77\t13\t9\t9.66666666666667\n+mz_1355.81\t12.3333333333333\t9\t9.66666666666667\n+mz_1355.86\t12\t9\t9\n+mz_1355.9\t11\t9\t8.66666666666667\n+mz_1355.95\t11.3333333333333\t9\t7.33333333333333\n+mz_1355.99\t9.66666666666667\t8\t8.66666666666667\n+mz_1356.03\t10\t9\t7.33333333333333\n+mz_1356.08\t10.3333333333333\t7.66666666666667\t9\n'

diff -r 000000000000 -r 28ba52c9548c test-data/msidata_1.RData

Binary file test-data/msidata_1.RData has changed

diff -r 000000000000 -r 28ba52c9548c test-data/msidata_2.RData

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diff -r 000000000000 -r 28ba52c9548c test-data/msidata_3.RData

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diff -r 000000000000 -r 28ba52c9548c test-data/pca_imzml.pdf

Binary file test-data/pca_imzml.pdf has changed

diff -r 000000000000 -r 28ba52c9548c test-data/pixel_annotation_file1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_annotation_file1.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -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

diff -r 000000000000 -r 28ba52c9548c test-data/pixel_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out2.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,10 @@
+spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz annotation
+xy_1_1 1 1 1 3672 42479 1267.525390625 col1
+xy_2_1 2 1 2 3672 29179 1264.42407226562 col2
+xy_3_1 3 1 3 3672 37005 1267.525390625 col3
+xy_1_2 1 2 4 3672 42306 1264.38171386719 col1
+xy_2_2 2 2 5 3672 30350 1267.525390625 col2
+xy_3_2 3 2 6 3672 35955 1199.55615234375 col3
+xy_1_3 1 3 7 3672 43872 1199.59753417969 col1
+xy_2_3 2 3 8 3672 33204 1267.48278808594 col2
+xy_3_3 3 3 9 3672 37961 1199.55615234375 col3

diff -r 000000000000 -r 28ba52c9548c test-data/pixel_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out3.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,10 @@
+spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz input m/z count
+xy_1_1 1 1 1 241 22.92 329.083343505859 0
+xy_2_1 2 1 2 332 29.26 328.916687011719 0
+xy_3_1 3 1 3 415 24.43 328.916687011719 0
+xy_1_2 1 2 4 343 39.62 329 0
+xy_2_2 2 2 5 301 18.34 328.916687011719 0
+xy_3_2 3 2 6 194 10.79 345.083343505859 0
+xy_1_3 1 3 7 308 14.68 328.916687011719 0
+xy_2_3 2 3 8 367 24.87 329 0
+xy_3_3 3 3 9 323 35.18 329.083343505859 0

diff -r 000000000000 -r 28ba52c9548c test-data/pixels_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test2.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -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

diff -r 000000000000 -r 28ba52c9548c test-data/pixels_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test4.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -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

diff -r 000000000000 -r 28ba52c9548c test-data/pixels_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test6.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -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 B
+xy_4_1 4 1 A
+xy_1_2 1 2 A
+xy_2_2 2 2 A
+xy_3_2 3 2 A
+xy_4_2 4 2 A
+xy_1_3 1 3 A
+xy_2_3 2 3 B
+xy_3_3 3 3 A
+xy_4_3 4 3 A
+xy_10_1 10 1 A
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+xy_12_1 12 1 A
+xy_13_1 13 1 B
+xy_10_2 10 2 B
+xy_11_2 11 2 B
+xy_12_2 12 2 A
+xy_13_2 13 2 B
+xy_10_3 10 3 A
+xy_11_3 11 3 A
+xy_12_3 12 3 B
+xy_13_3 13 3 A

diff -r 000000000000 -r 28ba52c9548c test-data/pixels_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test7.tabular Mon Oct 01 01:05:33 2018 -0400

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessed.RData

Binary file test-data/preprocessed.RData has changed

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessed.rdata

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diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results1.RData

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diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results1.pdf

Binary file test-data/preprocessing_results1.pdf has changed

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.txt Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,3 @@
+mz x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
+329 8.48069807321137 6.00276368862812 0 0 7.22240715797167 6.68463797360356 0 0 0
+345 0 0 4.70593890744759 0 0 0 5.23000350586712 4.17949067812964 5.08555910047608

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results2.RData

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diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results2.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.txt Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,297 @@\n+\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 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+++ b/test-data/preprocessing_results4.txt Mon Oct 01 01:05:33 2018 -0400

b'@@ -0,0 +1,160 @@\n+mz\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 3\n+1199\t1.90173968313755\t1.13259535967648\t2.08382650993109\t2.34349737625869\t1.33087314662273\t2.14468085106383\t3.43161925601751\t1.32706902782797\t2.22480967308554\n+1200\t1.39388874502695\t0.970046951574763\t1.52152411836238\t1.35619061126081\t1.10906095551895\t1.66382978723404\t2.22846006564551\t1.19804842790025\t1.7089117778773\n+1201\t1.13095882671438\t0.99102093971692\t1.23623834616944\t1.19344773790952\t1.05864909390445\t1.31063829787234\t1.67396061269147\t1.07824358511023\t1.28168383340797\n+1202\t1.09263589067539\t0.976548887898831\t1.13518929874341\t1.0033640618352\t0.953389126853377\t1.08663829787234\t1.32242888402626\t0.9820310805927\t1.04469323779669\n+1203\t1.10574636879399\t0.91761198121937\t1.07498986623429\t0.954758190327613\t0.902372322899506\t1.05106382978723\t1.17525984682713\t1.05059631369715\t1.11240483654277\n+1204\t1.06972857176487\t0.959559957503684\t1.0088366436968\t1.01262232307474\t0.972948929159802\t1.02127659574468\t1.20315919037199\t0.972262378026744\t1.04388714733542\n+1205\t0.994091198003719\t0.970046951574763\t1.02537494933117\t0.954758190327613\t0.983031301482702\t1.08936170212766\t1.08807439824945\t0.976870256595591\t0.931034482758621\n+1206\t0.886037806916359\t0.970046951574763\t0.955087150385083\t0.972840731811091\t0.947742998352554\t0.94468085106383\t1.05320021881838\t1.00912540657752\t0.959247648902821\n+1207\t1.05171967325031\t0.933342472325988\t1.01297122010539\t0.93305914054744\t0.917495881383855\t0.982978723404255\t1.00786378555799\t0.972262378026744\t0.983430362740708\n+1208\t1.00489653711246\t0.959559957503684\t1.04604783137414\t0.994539781591264\t1.00823723228995\t1.01276595744681\t1.05668763676149\t0.999909649439827\t0.991491267353336\n+1209\t1.34346382918619\t1.15356934781864\t1.26518038102959\t1.31640901999716\t1.0737726523888\t1.20425531914894\t1.19269693654267\t1.23951933501988\t1.12449619346171\n+1210\t1.2413173568116\t1.11749408821413\t1.25029590595865\t1.25333711530279\t1.12277298187809\t1.0743829787234\t1.08472647702407\t1.13685580050596\t1.07564711150918\n+1211\t1.12375526730855\t0.98577744268138\t1.09152817186867\t1.05240391433839\t0.967907742998353\t1.07659574468085\t0.997401531728665\t1.07824358511023\t1.07613076578594\n+1212\t1.05892323265614\t1.04869940710785\t0.979894608836644\t1.00900581477805\t0.993113673805601\t1\t0.979964442013129\t1.04138055655945\t1.06806986117331\n+1213\t0.990489418300808\t0.996264436752459\t1.0088366436968\t1.03432137285491\t1.01831960461285\t0.987234042553191\t0.986939277899344\t1.02294904228406\t1.08419167039857\n+1214\t1.07333035146778\t0.875664004935056\t1.06258613700851\t1.05240391433839\t0.967907742998353\t1.02127659574468\t1.0601750547046\t1.02294904228406\t1.08822212270488\n+1215\t1.15256950493185\t0.964803454539223\t1.11633563032023\t1.07048645582187\t1.0939373970346\t1.17021276595745\t1.13689824945295\t1.08745934224792\t1.205105239588\n+1216\t1.05532145295322\t0.98577744268138\t1.12873935954601\t1.02708835626152\t1.0031960461285\t1.08936170212766\t1.13341083150985\t1.04138055655945\t1.08419167039857\n+1217\t0.950869841568775\t0.975290448610302\t0.959221726793677\t0.961991206921004\t1.02840197693575\t0.970212765957447\t0.955552516411379\t0.972262378026744\t1.01970443349754\n+1218\t0.943666282162951\t0.970046951574763\t0.959221726793677\t0.9656077152177\t0.932619439868204\t0.906382978723404\t0.927653172866521\t1.05981207083484\t1.00761307657859\n+1219\t0.860825348995975\t0.933342472325988\t0.984029185245237\t0.969224223514395\t0.927578253706755\t0.957446808510638\t0.892778993435449\t0.944615106613661\t0.96730855351545\n+1220\t0.929259163351303\t0.938585969361527\t1.00056749087961\t0.889661040987094\t0.962866556836903\t1.00425531914894\t1.07761214442013\t0.986086013733285\t1.08016121809225\n+1221\t0.997692977706632\t0.975290448610302\t0.971625456019457\t0.940292157140831\t0.942701812191104\t1.0936170212766\t1.27290754923414\t1.08745934224792\t1.12449619346171\n+1222\t0.983285858894983\t0.975290448610302\t0.946817997567896\t0.918593107360658\t0.942701812191104\t1.05106382978723\t1.13689824945295\t1.0459884351283\t1.0237348858038'..b'1.02198251523589\n+1333\t1.07113796382253\t1.17089568584911\t1.04407042526568\t1.14721932750828\t1.0625943700308\t1.06123959296947\t1.05168395014746\t1.06261686648544\t1.026188204599\n+1334\t1.0297957967978\t1.08335208316881\t0.923268888458081\t1.08683936290258\t0.98894921567223\t0.981313598519889\t1.03712777090667\t1.0001099919863\t0.950485796063007\n+1335\t0.988453629773075\t0.957508154315864\t0.931897569658624\t0.913246964661195\t0.941605902156006\t0.945790934320074\t0.887926933688517\t0.995301770870979\t0.946280106699897\n+1336\t0.871943886339746\t0.935622253645788\t0.811096032851025\t0.886830730146202\t0.925824797650598\t0.941350601295097\t0.902483112929312\t0.971260665294386\t0.963102864152339\n+1337\t0.860668749878457\t0.979394054985941\t0.836982076452653\t0.943436946964045\t0.978428479335291\t0.914708603145236\t0.851536485586528\t0.937603117487155\t0.90001752370568\n+1338\t0.884073199805679\t1.08111375241846\t0.81188045841471\t0.883743118319774\t0.940410363935899\t0.923791102514507\t0.88643823353889\t0.929953674803693\t1.00248341000692\n+1339\t0.856910371058027\t0.946565203980826\t0.862868120054282\t0.924568208024764\t0.952126638492945\t0.945790934320074\t0.884287888878318\t0.952027780833111\t0.971514242878561\n+1340\t0.920802811005336\t0.935622253645788\t0.793838670449939\t0.909473216873339\t0.994209583840699\t0.959111933395005\t0.906122157739511\t0.865479800757373\t0.992542689694114\n+1341\t0.856910371058027\t0.968451104650903\t0.94915493205971\t0.901925721297627\t0.946866270324475\t0.892506938020352\t0.924317381790505\t0.91837023302588\t0.958897174789229\n+1342\t0.958386599209635\t0.913736352975711\t0.923268888458081\t0.966079433691182\t0.994209583840699\t0.892506938020352\t0.9388735610313\t0.961644223063748\t0.971514242878561\n+1343\t0.856910371058027\t0.962979629483384\t0.893068504256182\t0.939663199176188\t0.973168111166822\t0.932469935245143\t0.866092664827324\t0.923178454141198\t0.984131310967893\n+1344\t0.950869841568775\t0.99033700532098\t0.91895454785781\t0.958531938115469\t0.983688847503761\t0.892506938020352\t0.942512605841499\t0.889520906333967\t0.96730855351545\n+1345\t0.884073199805679\t0.966710180733965\t0.888558057264989\t0.919250654323694\t1.0009045978733\t0.974854932301741\t0.939700616669982\t0.919900121562572\t0.940927411146847\n+1346\t0.879460643980606\t0.946565203980826\t0.94915493205971\t0.920794460236907\t1.00999068834611\t0.905827937095282\t0.913400247359909\t0.985685328640342\t0.929457349247454\n+1347\t0.920802811005336\t0.935622253645788\t0.88875416365591\t0.943436946964045\t0.925824797650598\t0.910268270120259\t0.924317381790505\t0.971260665294386\t0.874783387527016\n+1348\t1.10120499438597\t1.00675143082354\t1.07858515006785\t1.10948184962972\t1.06785473819927\t1.16336725254394\t1.20452383217582\t1.06742508760076\t1.11030199186121\n+1349\t1.10120499438597\t0.984865530153461\t1.10015685306921\t1.10570810184186\t1.08889621087315\t1.06567992599445\t1.17177242888403\t1.13954840433054\t1.13974181740299\n+1350\t1.05610444854081\t1.01769438115858\t0.996612678662695\t0.973626929266894\t0.946866270324475\t0.967992599444958\t1.05532299495766\t1.0770415298314\t1.00936544714656\n+1351\t0.935152984683341\t1.00103125223931\t0.996808785053617\t0.907414808989054\t0.989905646248315\t0.960928433268859\t0.989158543863139\t1.02546243059434\t0.905752554655376\n+1352\t0.898252538082756\t0.962979629483384\t0.975040975661338\t0.947210694751901\t0.994209583840699\t0.910268270120259\t0.862453620017125\t0.956836001948429\t0.870577698163905\n+1353\t0.890735780441896\t0.957508154315864\t0.923268888458081\t0.962305685903325\t0.931085165819067\t0.874745605920444\t0.913400247359909\t0.947219559717792\t0.887400455616348\n+1354\t1.06362120618167\t1.11618093417392\t1.04838476586595\t1.07551811953901\t1.02051142468305\t1.08344125809436\t1.09535248786985\t1.11069907763863\t1.07245078759322\n+1355\t1.17876426640757\t1.01819178799199\t1.08701772487747\t1.1007336161215\t1.0558993559982\t1.09555125725338\t1.09948776606326\t1.05059631369714\t1.03765826649839\n+1356\t1.25341933661339\t1.11461765555463\t1.12696739822804\t1.128350588569\t1.02840197693575\t1.09422492401216\t1.08807439824945\t1.10589085652331\t0.953489859893801\n+1357\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\tNaN\n'

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results5.RData

Binary file test-data/preprocessing_results5.RData has changed

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results5.pdf

Binary file test-data/preprocessing_results5.pdf has changed

diff -r 000000000000 -r 28ba52c9548c test-data/preprocessing_results5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.txt Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,100 @@
+ x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
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diff -r 000000000000 -r 28ba52c9548c test-data/random_factors.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_factors.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,24 @@
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diff -r 000000000000 -r 28ba52c9548c test-data/rdata_notfiltered.RData

Binary file test-data/rdata_notfiltered.RData has changed

diff -r 000000000000 -r 28ba52c9548c test-data/rdata_notfiltered.pdf

Binary file test-data/rdata_notfiltered.pdf has changed

diff -r 000000000000 -r 28ba52c9548c test-data/scores_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scores_pca.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,10 @@
+pixel names x y PC1 PC2
+xy_1_1 1 1 1.00970093989579 0.757987492163095
+xy_2_1 2 1 0.579669229309751 -0.365615195586663
+xy_3_1 3 1 -1.04790449059337 0.831141108678224
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+xy_2_2 2 2 -0.325050824762022 0.275854508943195
+xy_3_2 3 2 -1.31374997886227 0.0192699346592569
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diff -r 000000000000 -r 28ba52c9548c test-data/sd_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sd_out2.tabular Mon Oct 01 01:05:33 2018 -0400

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diff -r 000000000000 -r 28ba52c9548c test-data/spectra_info_123_combi.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectra_info_123_combi.txt Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,13 @@
+x y column_name Number of Calibrants Number of Peaks TIC per spectrum Most abundant m/z
+1 1 column1 1 1798 121.850390398685 152.91667175293
+1 2 column1 2 2836 200.963327709254 153.08332824707
+1 3 column1 1 2405 127.846644478468 153.16667175293
+3 1 column2 1 2810 182.318354201019 153.08332824707
+3 2 column2 0 2540 135.305841731585 328.916687011719
+3 3 column2 0 2812 168.270181475225 153
+4 1 column3 1 2844 161.809190448268 153
+4 2 column3 0 2157 108.395974184216 171.25
+4 3 column3 1 3168 243.539506603108 153.08332824707
+9 1 column4 1 2844 161.809190448268 153
+9 2 column4 0 2157 108.395974184216 171.25
+9 3 column4 1 3168 243.539506603108 153.08332824707

diff -r 000000000000 -r 28ba52c9548c test-data/spectra_info_imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectra_info_imzml.txt Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,10 @@
+x y Number of Calibrants Number of Peaks TIC per spectrum Most abundant m/z
+1 1 1 1364 121.850390398685 328.971197672656
+1 2 2 1961 200.963327709254 328.971197672656
+1 3 1 1714 127.846644478468 153.173335465757
+2 1 1 1986 182.318354201019 153.112078382987
+2 2 0 1801 135.305841731585 328.971197672656
+2 3 0 1968 168.270181475225 255.28235280251
+3 1 1 1974 161.809190448268 152.989637701451
+3 2 0 1505 108.395974184216 255.28235280251
+3 3 1 2180 243.539506603108 153.112078382987

diff -r 000000000000 -r 28ba52c9548c test-data/tabular_LM8file16.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_LM8file16.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,2 @@
+inputmz countpixels percentpixels
+1111.1 0 0

diff -r 000000000000 -r 28ba52c9548c test-data/tabular_analyze75.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_analyze75.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,3 @@
+inputmz countpixels percentpixels
+1296.7 9 100
+1305.1 9 100

diff -r 000000000000 -r 28ba52c9548c test-data/tabular_imzml.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_imzml.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,4 @@
+inputmz countpixels percentpixels
+152 9 100
+328.9 9 100
+185.2 6 66.7

diff -r 000000000000 -r 28ba52c9548c test-data/tabular_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_rdata.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,2 @@
+inputmz countpixels percentpixels
+328.9 9 100

diff -r 000000000000 -r 28ba52c9548c test-data/test1.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test2.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test2.rdata

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diff -r 000000000000 -r 28ba52c9548c test-data/test3.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test4.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test4.rdata

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diff -r 000000000000 -r 28ba52c9548c test-data/test5.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test6.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/test6.rdata

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diff -r 000000000000 -r 28ba52c9548c test-data/test7.pdf

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diff -r 000000000000 -r 28ba52c9548c test-data/toplabels_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_skm.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,21 @@
+mz r k cluster centers withinss betweenss
+1199.55615234375 3 3 1 81 154 3661.33333333333
+1199.55615234375 3 3 2 12.3333333333333 18.6666666666667 3661.33333333333
+1199.55615234375 3 3 3 37 0 3661.33333333333
+1199.59753417969 3 3 1 84 137.2 3658.13333333333
+1199.59753417969 3 3 2 14.3333333333333 144.666666666667 3658.13333333333
+1199.59753417969 3 3 3 34.6 0 3658.13333333333
+1199.55615234375 1 3 1 49.3333333333333 1504.66666666667 2198
+1199.55615234375 1 3 2 12.3333333333333 112.666666666667 2198
+1199.55615234375 1 3 3 39.3333333333333 18.6666666666667 2198
+1199.55615234375 2 3 1 49.3333333333333 1504.66666666667 2198
+1199.55615234375 2 3 2 12.3333333333333 112.666666666667 2198
+1199.55615234375 2 3 3 39.3333333333333 18.6666666666667 2198
+1199.63891601562 3 3 1 62 45.2 2049.02222222222
+1199.63891601562 3 3 2 11 26 2049.02222222222
+1199.63891601562 3 3 3 30.4 0 2049.02222222222
+1199.55615234375 2 2 1 44.3333333333333 1767.33333333333 2048
+1199.55615234375 2 2 2 12.3333333333333 18.6666666666667 2048
+1199.55615234375 3 2 1 44.3333333333333 1767.33333333333 2048
+1199.55615234375 3 2 2 12.3333333333333 18.6666666666667 2048
+1199.59753417969 1 3 1 48 1946 1784.66666666667

diff -r 000000000000 -r 28ba52c9548c test-data/toplabels_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_ssc.tabular Mon Oct 01 01:05:33 2018 -0400

@@ -0,0 +1,51 @@
+mz r k s classes centers tstatistics p.values adj.p.values
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+364.333343505859 2 3 2 1 15.8337765722821 0.449479909587349 NA NA
+203.833343505859 1 3 2 1 14.0415253451331 0.449478654505296 NA NA
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+259.916656494141 1 3 2 1 13.8981327063543 0.449478540011514 NA NA
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+200.25 1 3 2 1 10.4880169699887 0.449474897701911 NA NA
+200.25 2 3 2 1 10.4880169699887 0.449474897701911 NA NA
+200.333343505859 1 3 2 1 10.2892503590812 0.449474610932727 NA NA
+200.333343505859 2 3 2 1 10.2892503590812 0.449474610932727 NA NA
+259.833343505859 1 3 2 1 9.55638913925806 0.449473448172064 NA NA
+259.833343505859 2 3 2 1 9.55638913925806 0.449473448172064 NA NA
+360.916687011719 1 3 2 1 9.04224883162212 0.449472524177856 NA NA
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+370.083343505859 1 3 2 1 8.45643021892373 0.44947133139287 NA NA
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+364.25 1 3 2 1 8.15357261143537 0.449470647536679 NA NA
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+200.16667175293 1 3 2 1 6.16326174971333 0.449464481313509 NA NA
+200.16667175293 2 3 2 1 6.16326174971333 0.449464481313509 NA NA
+203.91667175293 1 3 2 1 6.03716112636297 0.449463953687195 NA NA
+203.91667175293 2 3 2 1 6.03716112636297 0.449463953687195 NA NA
+225 1 3 2 1 5.71436916011582 0.449462496977867 NA NA
+225 2 3 2 1 5.71436916011582 0.449462496977867 NA NA
+216.91667175293 1 3 2 1 5.64877209898622 0.449462180580643 NA NA
+216.91667175293 2 3 2 1 5.64877209898622 0.449462180580643 NA NA
+249.25 1 3 2 1 5.15263210866428 0.449459526788925 NA NA
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+367.583343505859 1 3 2 1 4.44314020180342 0.449454702074192 NA NA
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+364.416687011719 1 3 2 1 4.30740701190317 0.449453597945591 NA NA
+364.416687011719 2 3 2 1 4.30740701190317 0.449453597945591 NA NA
+370 1 3 2 1 4.15967192336677 0.449452314295502 NA NA
+370 2 3 2 1 4.15967192336677 0.449452314295502 NA NA
+249.333343505859 1 3 2 1 4.06900916364662 0.449451480388054 NA NA
+249.333343505859 2 3 2 1 4.06900916364662 0.449451480388054 NA NA
+260 1 3 2 1 4.06636831188445 0.449451455520709 NA NA
+260 2 3 2 1 4.06636831188445 0.449451455520709 NA NA
+361 1 3 2 1 3.70261707034987 0.449447694373555 NA NA
+361 2 3 2 1 3.70261707034987 0.449447694373555 NA NA
+250.583343505859 1 3 2 1 3.44558838817237 0.449444557922452 NA NA
+250.583343505859 2 3 2 1 3.44558838817237 0.449444557922452 NA NA
+360.833343505859 1 3 2 1 3.35278414565422 0.449443307303055 NA NA
+360.833343505859 2 3 2 1 3.35278414565422 0.449443307303055 NA NA
+370.166687011719 1 3 2 1 2.82853938684749 0.449434701602457 NA NA
+370.166687011719 2 3 2 1 2.82853938684749 0.449434701602457 NA NA
+367.666687011719 1 3 2 1 2.5012261861986 0.449427499520948 NA NA
+367.666687011719 2 3 2 1 2.5012261861986 0.449427499520948 NA NA
+225.083343505859 1 3 2 1 2.45608703725853 0.449426355692286 NA NA
+225.083343505859 2 3 2 1 2.45608703725853 0.449426355692286 NA NA

diff -r 000000000000 -r 28ba52c9548c test-data/xy_coordinates.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates.tabular Mon Oct 01 01:05:33 2018 -0400

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