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Changeset 0:9c03e7a617cd (2018-10-01)

Next changeset 1:1d9931768896 (2018-10-25)

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

added:
macros.xml
spectra_plots.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 9c03e7a617cd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 01 01:08:16 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 9c03e7a617cd spectra_plots.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/spectra_plots.xml Mon Oct 01 01:08:16 2018 -0400

[

b'@@ -0,0 +1,455 @@\n+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">\n+ <description>\n+ mass spectrometry imaging mass spectra plots\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+ <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="0.5.0">r-scales</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ @INPUT_LINKING@\n+ cat \'${MSI_mzplots}\' &&\n+ Rscript \'${MSI_mzplots}\'\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_mzplots"><![CDATA[\n+\n+################################# load libraries and read file #################\n+\n+library(Cardinal)\n+library(gridExtra)\n+library(ggplot2)\n+library(scales)\n+\n+@READING_MSIDATA@\n+\n+@DATA_PROPERTIES@\n+\n+######################################## PDF ###################################\n+################################################################################\n+################################################################################\n+\n+\n+pdf("mzplots.pdf", fonts = "Times", pointsize = 12)\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n+#if not $filename:\n+ #set $filename = $infile.display_name\n+#end if\n+title(main=paste0("Mass spectra for file: \\n\\n","$filename"))\n+\n+\n+############################# I) numbers ######################################\n+###############################################################################\n+\n+grid.table(property_df, rows= NULL)\n+\n+## set NA to 0 otherwise plot function will not work\n+\n+ spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero\n+\n+if (npeaks > 0){\n+\n+ pixeldf = data.frame(matrix(ncol = 2, nrow=0))\n+\n+ ############################# single pixel ################################\n+ ###########################################################################\n+\n+ #if str( $pixel_conditional.pixel_type) == \'single_pixel\':\n+ print("single_pixel")\n+\n+ #for $chosenpixel in $pixel_conditional.repeatpixel: \n+\n+ pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy)\n+ pixelisvalid = as.character(pixelname %in% names(pixels(msidata)))\n+ pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))\n+\n+ ############################# II) control image ####################\n+\n+ if (pixelisvalid == "TRUE"){\n+ print(pixelisvalid)\n+\n+ image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),\n+ colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,\n+ main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))\n+\n+ abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)\n+ abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)\n+\n+ ##################### III) plot full mass spectrum #################\n+\n+ plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))\n+\n+ ##################### IV) plot zoom-in mass spectrum ###############\n+\n+ #if $chosenpixel.zoomedplot:\n+ iData(msidata) <- iData(msidata)[] ## getting back data on disk \n+\n+ #for $token in $chosenpixel.zoomedplot:\n+\n+ minmasspixel = features(msidata, mz=$token.xlimmin)\n+ maxmasspixel = features(msidata, mz=$token.xlimmax)\n+\n+ plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), \n+ '..b' </conditional>\n+ <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <expand macro="infile_analyze75"/>\n+ <conditional name="pixel_conditional">\n+ <param name="pixel_type" value="sample_pixel"/>\n+ <conditional name="tabular_annotation">\n+\n+ <param name="load_annotation" value="yes_annotation"/>\n+ <param name="annotation_file" value="annotations.tabular" ftype="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+\n+\n+\n+ </conditional>\n+ <repeat name="zoomed_sample">\n+ <param name="xlimmin" value="1250"/>\n+ <param name="xlimmax" value="1270"/>\n+ </repeat>\n+ </conditional>\n+ <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="3_files_combined.RData" ftype="rdata"/>\n+ <conditional name="pixel_conditional">\n+ <param name="pixel_type" value="sample_pixel"/>\n+ <repeat name="zoomed_sample">\n+ <param name="xlimmin" value="350"/>\n+ <param name="xlimmax" value="360"/>\n+ </repeat>\n+ </conditional>\n+ <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>\n+ <conditional name="pixel_conditional">\n+ <param name="pixel_type" value="single_pixel"/>\n+ <repeat name="repeatpixel">\n+ <param name="plusminusinDalton" value="0.1"/>\n+ <param name="inputx" value="1"/>\n+ <param name="inputy" value="1"/>\n+ </repeat>\n+ </conditional>\n+ <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.\n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+@SPECTRA_TABULAR_INPUT_DESCRIPTION@\n+\n+**Options**\n+\n+- "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates\n+\n+ - Enter the x and y coordinates of your pixel of interest\n+ - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type.\n+ - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot\n+\n+- "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted\n+\n+ - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot\n+\n+\n+**Tip** \n+\n+- Corresponding m/z intensity pairs for single spectra can be obtained with the filtering tool option "ranges for x and y" and afterwards using the imzml tabular exporter tool\n+- Plots will only be drawn for pixels that exist in the MSI data, pixel that are outside the dataset will be "False" in the overview table on the last page of the pdf\n+\n+\n+**Output**\n+\n+- Pdf with the selected mass spectra plots and additional x-y grid plots\n+\n+\n+]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 9c03e7a617cd 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 01:08:16 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

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diff -r 000000000000 -r 9c03e7a617cd test-data/123_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd 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 01:08:16 2018 -0400

@@ -0,0 +1,13 @@
+x y sample_name file_name column_name NA.x NA.y NA
+1 1 File1 file_one col1 NA NA NA
+1 2 File1 file_one col1 NA NA NA
+1 3 File1 file_one col1 NA NA NA
+3 1 File2 file_two col2 NA NA NA
+3 2 File2 file_two col2 NA NA NA
+3 3 File2 file_two col2 NA NA NA
+4 1 File2 file_two col3 NA NA NA
+4 2 File2 file_two col3 NA NA NA
+4 3 File2 file_two col3 NA NA NA
+9 1 File3 file_three col3 NA NA NA
+9 2 File3 file_three col3 NA NA NA
+9 3 File3 file_three col3 NA NA 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 9c03e7a617cd test-data/features_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out3.tabular Mon Oct 01 01:08:16 2018 -0400

diff -r 000000000000 -r 9c03e7a617cd test-data/features_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test2.tabular Mon Oct 01 01:08:16 2018 -0400

b'@@ -0,0 +1,101 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diff -r 000000000000 -r 9c03e7a617cd test-data/features_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test4.tabular Mon Oct 01 01:08:16 2018 -0400

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diff -r 000000000000 -r 9c03e7a617cd test-data/features_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test6.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,21 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/features_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test7.tabular Mon Oct 01 01:08:16 2018 -0400

diff -r 000000000000 -r 9c03e7a617cd test-data/featuresofinterest5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:08:16 2018 -0400

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diff -r 000000000000 -r 9c03e7a617cd test-data/imzml_filtered.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/imzml_filtered.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/imzml_filtered4.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/imzml_filtered5.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/inputcalibrantfile1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/inputcalibrantfile2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/inputpeptides.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/inputpeptides2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,4 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/inputpixels_2column.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,6 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/int_matrix1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix1.tabular Mon Oct 01 01:08:16 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 9c03e7a617cd test-data/int_matrix3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix3.tabular Mon Oct 01 01:08:16 2018 -0400

diff -r 000000000000 -r 9c03e7a617cd test-data/kmeans_analyze.pdf

Binary file test-data/kmeans_analyze.pdf has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/loadings_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loadings_pca.tabular Mon Oct 01 01:08:16 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 9c03e7a617cd test-data/mean_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_out2.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/msidata_1.RData

Binary file test-data/msidata_1.RData has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/msidata_2.RData

Binary file test-data/msidata_2.RData has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/msidata_3.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/pca_imzml.pdf

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diff -r 000000000000 -r 9c03e7a617cd 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 01:08:16 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 9c03e7a617cd test-data/pixel_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out2.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/pixel_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out3.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/pixels_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test2.tabular Mon Oct 01 01:08:16 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
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+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
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+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 9c03e7a617cd test-data/pixels_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test4.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/pixels_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test6.tabular Mon Oct 01 01:08:16 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
+xy_11_1 11 1 A
+xy_12_1 12 1 A
+xy_13_1 13 1 B
+xy_10_2 10 2 B
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+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 9c03e7a617cd test-data/pixels_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test7.tabular Mon Oct 01 01:08:16 2018 -0400

diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessed.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessed.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results1.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results1.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.txt Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/preprocessing_results2.RData

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results2.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.txt Mon Oct 01 01:08:16 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.txt Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/preprocessing_results5.RData

Binary file test-data/preprocessing_results5.RData has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results5.pdf

Binary file test-data/preprocessing_results5.pdf has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/preprocessing_results5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.txt Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/random_factors.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_factors.tabular Mon Oct 01 01:08:16 2018 -0400

@@ -0,0 +1,24 @@
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diff -r 000000000000 -r 9c03e7a617cd test-data/rdata_notfiltered.RData

Binary file test-data/rdata_notfiltered.RData has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/rdata_notfiltered.pdf

Binary file test-data/rdata_notfiltered.pdf has changed

diff -r 000000000000 -r 9c03e7a617cd test-data/scores_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scores_pca.tabular Mon Oct 01 01:08:16 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
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diff -r 000000000000 -r 9c03e7a617cd test-data/sd_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sd_out2.tabular Mon Oct 01 01:08:16 2018 -0400

b'@@ -0,0 +1,3673 @@\n+mz 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diff -r 000000000000 -r 9c03e7a617cd 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 01:08:16 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 9c03e7a617cd 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 01:08:16 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 9c03e7a617cd test-data/tabular_LM8file16.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_LM8file16.tabular Mon Oct 01 01:08:16 2018 -0400

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

diff -r 000000000000 -r 9c03e7a617cd test-data/tabular_analyze75.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_analyze75.tabular Mon Oct 01 01:08:16 2018 -0400

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

diff -r 000000000000 -r 9c03e7a617cd test-data/tabular_imzml.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_imzml.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/tabular_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_rdata.tabular Mon Oct 01 01:08:16 2018 -0400

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

diff -r 000000000000 -r 9c03e7a617cd test-data/test1.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test2.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test2.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/test3.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test4.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test4.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/test5.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test6.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test6.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/test7.pdf

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diff -r 000000000000 -r 9c03e7a617cd test-data/test7.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/testfile_squares.rdata

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diff -r 000000000000 -r 9c03e7a617cd test-data/toplabels_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_skm.tabular Mon Oct 01 01:08:16 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 9c03e7a617cd test-data/toplabels_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_ssc.tabular Mon Oct 01 01:08:16 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
+259.916656494141 2 3 2 1 13.8981327063543 0.449478540011514 NA NA
+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
+364.25 2 3 2 1 8.15357261143537 0.449470647536679 NA NA
+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
+367.583343505859 2 3 2 1 4.44314020180342 0.449454702074192 NA NA
+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 9c03e7a617cd test-data/xy_coordinates.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates.tabular Mon Oct 01 01:08:16 2018 -0400

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