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Changeset 0:93be1d20b5c3 (2018-10-01)

Next changeset 1:65245dc812c3 (2018-10-25)

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

added:
combine.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 93be1d20b5c3 combine.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/combine.xml Mon Oct 01 01:08:54 2018 -0400

[

b'@@ -0,0 +1,554 @@\n+<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0">\n+ <description>\n+ combine several mass spectrometry imaging datasets into one\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="3.0.0">r-ggplot2</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ #for $i, $infile in enumerate($infiles):\n+ #if $infile.ext == \'imzml\'\n+ ln -s \'${infile.extra_files_path}/imzml\' infile_${i}.imzML &&\n+ ln -s \'${infile.extra_files_path}/ibd\' infile_${i}.ibd &&\n+ #elif $infile.ext == \'analyze75\'\n+ ln -s \'${infile.extra_files_path}/hdr\' infile_${i}.hdr &&\n+ ln -s \'${infile.extra_files_path}/img\' infile_${i}.img &&\n+ ln -s \'${infile.extra_files_path}/t2m\' infile_${i}.t2m &&\n+ #else\n+ ln -s \'$infile\' infile_${i}.RData &&\n+ #end if\n+ #end for\n+ #if $annotation_cond.annotation_tabular == \'annotation\'\n+ #for $i, $annotation_file in enumerate($annotation_cond.annotation_files):\n+ ln -s \'$annotation_file\' annotation_file_${i}.tabular &&\n+ #end for\n+ #end if\n+\n+ cat \'${msi_combine}\' &&\n+ Rscript \'${msi_combine}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="msi_combine"><![CDATA[\n+\n+#import re\n+\n+################ load libraries and some preparations #################\n+\n+library(Cardinal)\n+library(ggplot2)\n+\n+## read tabular file for xy_shift option\n+#if str( $combine_conditional.combine_method ) == \'xy_shifts\':\n+ input_list = read.delim("$combine_conditional.coordinates_file", header = $combine_conditional.xy_header, \n+ stringsAsFactors = FALSE)\n+#end if\n+\n+## function to load RData and store with new variable name\n+loadRData <- function(fileName){\n+load(fileName)\n+get(ls()[ls() != "fileName"])\n+}\n+\n+## preparations for reading files one by one with for loop\n+pixel_vector = numeric()\n+x_shifts = 0\n+y_shifts = 0\n+max_y = numeric()\n+valid_dataset = logical()\n+#set $msidata = []\n+#set $pixelcoords = []\n+#set $num_infiles = len($infiles)\n+all_files = $num_infiles\n+\n+\n+############## reading files and changing pixel coordinates ###################\n+\n+#for $i, $infile in enumerate($infiles):\n+\n+ ## read and manipulate MSI data\n+\n+ #if $infile.ext == \'imzml\'\n+ #if str($processed_cond.processed_file) == "processed":\n+ msidata_$i <- readImzML(\'infile_${i}\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")\n+ centroided(msidata) = $centroids\n+ #else\n+ msidata_$i <- readImzML(\'infile_${i}\')\n+ centroided(msidata) = $centroids\n+ #end if\n+ #elif $infile.ext == \'analyze75\'\n+ msidata_$i <- readAnalyze(\'infile_${i}\')\n+ centroided(msidata) = $centroids\n+ #else\n+ msidata_$i = loadRData(\'infile_${i}.RData\')\n+ #end if\n+\n+ ## remove duplicated coordinates, otherwise combine will fail\n+ print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file"))\n+ msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))]\n+\n+ ## same name for MSI data files necessary to combine data in one single coordinate system\n+ sampleNames(msidata_$i) = "msidata"\n+\n+\n+ ## read and process annotation tabular or automatically use name of infile as annotation\n+\n+ ## set all pixel annotations to NA, necessary in case files were combined before with different annotations\n+ msidata_$i\\$column1 = rep(NA, ncol(msidata_$i))\n+ msidata_$i\\$column2 = rep(NA, ncol(msidata_$i))\n+ msidata_$i\\$column3 = rep(NA, ncol(msidata_$i))\n+ msidata_$i\\$column4 = rep(NA, ncol(msidata_$i))\n+ msidata_$i\\$column5 = rep(NA, ncol(msidata_$i))\n+ '..b'output.tabular"/>\n+ <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />\n+ <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="infiles" value="msidata_2.RData,123_combined.RData" ftype="rdata"/>\n+ <conditional name="annotation_cond">\n+ <param name="annotation_tabular" value="no_annotation"/>\n+ </conditional>\n+ <param name="combine_method" value="automatic_combine"/>\n+ <output name="pixel_annotations" file="2123_annotation_output.tabular"/>\n+ <output name="msidata_combined" file="2123_auto_combined.RData" compare="sim_size" />\n+ <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool uses the Cardinal combine function to combine several mass spectrometry imaging data. \n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+- MSI data files must have the same m/z values (to obtain same m/z values for different files: filtering tool same m/z range and preprocessing tool same binning width)\n+- Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts. \n+@SPECTRA_TABULAR_INPUT_DESCRIPTION@\n+\n+- For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name\n+\n+ - Each input file is shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260.\n+ - The file can have any column names as header (in this case set "Tabular file contains a header line" to yes) or no header at all\n+\n+ ::\n+ \n+ x_shift y_shift file name\n+ 0 0 file1\n+ 510 0 file2\n+ 0 260 file3\n+ 510 260 file4\n+ ...\n+ ...\n+ \n+\n+\n+\n+**Options**\n+\n+- "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name\n+- "xy shifts": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).\n+\n+**Tips**\n+\n+- The combine tools puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. \'MSI classification\') or useful (e.g. \'MSI spectra plots\').\n+- In case more annotations are required: The annotation input file should have an identifier column, for example the patient_ID. A second tabular file that contains more annotations and also one column with the identifier column (e.g. \'patient_ID\') can be merged to the annotation output file of this tool with the tool \'join two files\' and then set the \'Column to use\' parameters for both files to the identifier column. \n+\n+\n+\n+**Output**\n+\n+- single imzML file containing all valid input files\n+- pdf that shows the pixel positions and annotations of the combined files\n+- Tabular file with pixel annotations (x,y,column with input file names and up to five annotation columns)\n+\n+\n+]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 93be1d20b5c3 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 01 01:08:54 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 93be1d20b5c3 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 01:08:54 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 93be1d20b5c3 test-data/112_auto_combined.RData

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

diff -r 000000000000 -r 93be1d20b5c3 test-data/112_auto_combined_QC.pdf

Binary file test-data/112_auto_combined_QC.pdf has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/123_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.tabular Mon Oct 01 01:08:54 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 93be1d20b5c3 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 01:08:54 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
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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 93be1d20b5c3 test-data/features_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out3.tabular Mon Oct 01 01:08:54 2018 -0400

diff -r 000000000000 -r 93be1d20b5c3 test-data/features_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test2.tabular Mon Oct 01 01:08:54 2018 -0400

b'@@ -0,0 +1,101 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diff -r 000000000000 -r 93be1d20b5c3 test-data/features_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test4.tabular Mon Oct 01 01:08:54 2018 -0400

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diff -r 000000000000 -r 93be1d20b5c3 test-data/features_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test6.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,21 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/features_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test7.tabular Mon Oct 01 01:08:54 2018 -0400

diff -r 000000000000 -r 93be1d20b5c3 test-data/featuresofinterest5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:08:54 2018 -0400

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diff -r 000000000000 -r 93be1d20b5c3 test-data/imzml_filtered.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/imzml_filtered3.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/imzml_filtered4.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/imzml_filtered5.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/inputcalibrantfile1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/inputcalibrantfile2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/inputpeptides.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,3 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/inputpeptides2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,4 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/inputpixels_2column.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,6 @@
+1 A 1
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diff -r 000000000000 -r 93be1d20b5c3 test-data/int_matrix1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix1.tabular Mon Oct 01 01:08:54 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 93be1d20b5c3 test-data/int_matrix3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix3.tabular Mon Oct 01 01:08:54 2018 -0400

diff -r 000000000000 -r 93be1d20b5c3 test-data/kmeans_analyze.pdf

Binary file test-data/kmeans_analyze.pdf has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/loadings_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loadings_pca.tabular Mon Oct 01 01:08:54 2018 -0400

b'@@ -0,0 +1,1200 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diff -r 000000000000 -r 93be1d20b5c3 test-data/mean_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_out2.tabular Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/msidata_1.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/msidata_2.RData

Binary file test-data/msidata_2.RData has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/msidata_3.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/pca_imzml.pdf

Binary file test-data/pca_imzml.pdf has changed

diff -r 000000000000 -r 93be1d20b5c3 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 01:08:54 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 93be1d20b5c3 test-data/pixel_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out2.tabular Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/pixel_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out3.tabular Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/pixels_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test2.tabular Mon Oct 01 01:08:54 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
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+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
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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 93be1d20b5c3 test-data/pixels_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test4.tabular Mon Oct 01 01:08:54 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
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+xy_3_3 3 3 C
+xy_4_3 4 3 A
+xy_10_1 10 1 A
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+xy_12_1 12 1 C
+xy_13_1 13 1 B
+xy_10_2 10 2 B
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+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 93be1d20b5c3 test-data/pixels_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test6.tabular Mon Oct 01 01:08:54 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
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+xy_1_3 1 3 A
+xy_2_3 2 3 B
+xy_3_3 3 3 A
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+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
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+xy_12_2 12 2 A
+xy_13_2 13 2 B
+xy_10_3 10 3 A
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+xy_12_3 12 3 B
+xy_13_3 13 3 A

diff -r 000000000000 -r 93be1d20b5c3 test-data/pixels_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test7.tabular Mon Oct 01 01:08:54 2018 -0400

diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessed.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessed.rdata

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results1.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results1.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.txt Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/preprocessing_results2.RData

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results2.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.txt Mon Oct 01 01:08:54 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 01:08:54 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 93be1d20b5c3 test-data/preprocessing_results5.RData

Binary file test-data/preprocessing_results5.RData has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results5.pdf

Binary file test-data/preprocessing_results5.pdf has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/preprocessing_results5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.txt Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/random_factors.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_factors.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,24 @@
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diff -r 000000000000 -r 93be1d20b5c3 test-data/rdata_notfiltered.RData

Binary file test-data/rdata_notfiltered.RData has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/rdata_notfiltered.pdf

Binary file test-data/rdata_notfiltered.pdf has changed

diff -r 000000000000 -r 93be1d20b5c3 test-data/scores_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scores_pca.tabular Mon Oct 01 01:08:54 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
+xy_1_2 1 2 3.5004093695087 0.608578545994517
+xy_2_2 2 2 -0.325050824762022 0.275854508943195
+xy_3_2 3 2 -1.31374997886227 0.0192699346592569
+xy_1_3 1 3 -1.46193831394872 -0.0337353199555284
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+xy_3_3 3 3 0.147195401291175 -3.25809198000829

diff -r 000000000000 -r 93be1d20b5c3 test-data/sd_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sd_out2.tabular Mon Oct 01 01:08:54 2018 -0400

b'@@ -0,0 +1,3673 @@\n+mz 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diff -r 000000000000 -r 93be1d20b5c3 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 01:08:54 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 93be1d20b5c3 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 01:08:54 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 93be1d20b5c3 test-data/tabular_LM8file16.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_LM8file16.tabular Mon Oct 01 01:08:54 2018 -0400

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

diff -r 000000000000 -r 93be1d20b5c3 test-data/tabular_analyze75.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_analyze75.tabular Mon Oct 01 01:08:54 2018 -0400

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

diff -r 000000000000 -r 93be1d20b5c3 test-data/tabular_imzml.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_imzml.tabular Mon Oct 01 01:08:54 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 93be1d20b5c3 test-data/tabular_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_rdata.tabular Mon Oct 01 01:08:54 2018 -0400

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

diff -r 000000000000 -r 93be1d20b5c3 test-data/test1.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test2.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test2.rdata

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test3.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test4.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test4.rdata

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test5.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test6.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test6.rdata

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diff -r 000000000000 -r 93be1d20b5c3 test-data/test7.pdf

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diff -r 000000000000 -r 93be1d20b5c3 test-data/toplabels_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_skm.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,21 @@
+mz r k cluster centers withinss betweenss
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+1199.55615234375 3 3 3 37 0 3661.33333333333
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+1199.59753417969 3 3 3 34.6 0 3658.13333333333
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+1199.63891601562 3 3 1 62 45.2 2049.02222222222
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+1199.63891601562 3 3 3 30.4 0 2049.02222222222
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+1199.55615234375 3 2 2 12.3333333333333 18.6666666666667 2048
+1199.59753417969 1 3 1 48 1946 1784.66666666667

diff -r 000000000000 -r 93be1d20b5c3 test-data/toplabels_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_ssc.tabular Mon Oct 01 01:08:54 2018 -0400

@@ -0,0 +1,51 @@
+mz r k s classes centers tstatistics p.values adj.p.values
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+200.25 1 3 2 1 10.4880169699887 0.449474897701911 NA NA
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+259.833343505859 1 3 2 1 9.55638913925806 0.449473448172064 NA NA
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+203.91667175293 1 3 2 1 6.03716112636297 0.449463953687195 NA NA
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+225 1 3 2 1 5.71436916011582 0.449462496977867 NA NA
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+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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+370 1 3 2 1 4.15967192336677 0.449452314295502 NA NA
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+361 1 3 2 1 3.70261707034987 0.449447694373555 NA NA
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+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 93be1d20b5c3 test-data/xy_coordinates.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates.tabular Mon Oct 01 01:08:54 2018 -0400

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