Galaxy |

Changeset 0:5f18275c250a (2018-10-01)

Next changeset 1:ae9ffc7ba261 (2018-10-25)

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

added:
macros.xml
quality_report.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 5f18275c250a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 01 01:07:13 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 5f18275c250a quality_report.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/quality_report.xml Mon Oct 01 01:07:13 2018 -0400

[

b'@@ -0,0 +1,987 @@\n+<tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.0">\n+ <description>\n+ mass spectrometry imaging QC\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n+ <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+ <requirement type="package" version="2.23_15">r-kernsmooth</requirement>\n+ <requirement type="package" version="0.5.0">r-scales</requirement>\n+ <requirement type="package" version="1.0.8"> r-pheatmap</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ @INPUT_LINKING@\n+ cat \'${cardinal_qualitycontrol_script}\' &&\n+ Rscript \'${cardinal_qualitycontrol_script}\'\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="cardinal_qualitycontrol_script"><![CDATA[\n+\n+################################# load libraries and read file #################\n+\n+library(Cardinal)\n+library(ggplot2)\n+library(RColorBrewer)\n+library(gridExtra)\n+library(KernSmooth)\n+library(scales)\n+library(pheatmap)\n+\n+@READING_MSIDATA@\n+\n+## remove duplicated coordinates\n+print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))\n+msidata <- msidata[,!duplicated(coord(msidata))]\n+\n+## create full matrix to make processed imzML files compatible with segmentation and other steps\n+iData(msidata) <- iData(msidata)[]\n+\n+## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)\n+\n+#if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n+\n+ ## read and extract x,y,annotation information\n+ input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)\n+ annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]\n+ annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name\n+ colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"\n+\n+ ## merge with coordinate information of msidata\n+ msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))\n+ colnames(msidata_coordinates)[3] = "pixel_index"\n+ merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)\n+ merged_annotation[is.na(merged_annotation)] = "NA"\n+ merged_annotation = merged_annotation[order(merged_annotation\\$pixel_index),]\n+ msidata\\$annotation = as.factor(merged_annotation[,4])\n+\n+#end if\n+\n+###################### calculation of data properties ################################\n+@DATA_PROPERTIES@\n+\n+## Median intensities\n+medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)\n+## Spectra multiplied with m/z (potential number of peaks)\n+numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n+## Percentage of intensities > 0\n+percpeaks = round(npeaks/numpeaks*100, digits=2)\n+## Number of empty TICs\n+TICs = colSums(spectra(msidata)[], na.rm=TRUE) \n+NumemptyTIC = sum(TICs == 0)\n+## Median und sd TIC\n+medTIC = round(median(TICs), digits=1)\n+sdTIC = round(sd(TICs), digits=0)\n+## Median and sd # peaks per spectrum\n+medpeaks = round(median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)\n+sdpeaks = round(sd(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)\n+print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))\n+## Processing informations\n+centroidedinfo = centroided(msidata)\n+\n+############## Read and filter tabular file with m/z ###########################\n+\n+### reading calibrant file: \n+\n+#if $calibrant_file:\n+\n+ calibrant_list '..b'mponents: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels. \n+\n+**Properties over spectra/pixels**\n+\n+- Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. If annotation tabular file is provided, the pixels are sorted according to annotation groups and the dotted lines in the scatter plot separate spectra of different annotation groups.\n+- (annot) Number of peaks per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.\n+- TIC per spectrum: Scatter plot and histogram showing the sum of all intensities per spectrum (TIC). Dotted lines in the scatter plot separate spectra of different annotation groups.\n+- (annot) TIC per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group. \n+\n+**Properties over m/z features**\n+\n+- Histogram of m/z values: Histogram of all m/z values (complete m/z axis)\n+- Number of peaks per m/z: Scatter plot and histogram giving the number of intensities > 0 for each m/z. \n+- Sum of intensities per m/z: Scatter plot and histogram of the sum of all intensities per m/z. \n+\n+**Intensity plots**\n+\n+- Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups.\n+- Log2-transformed intensities: Histogram of log2-transformed intensities. \n+- (annot) log2-transformed intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group. \n+- (annot) Mean intensities per m/z and annotation group: For all pixels of an annotation group the mean intensity for each m/z is calculated and shown as boxplot. \n+- (annot) Pearson correlation between annotation groups based on mean intensities and shown as heatmap.\n+\n+**Mass spectra and m/z accuracy**\n+\n+- Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from random individual pixels (spectra). \n+- (cal) For each calibrant four zoomed in mass spectrum are drawn: The first shows the average intensities over all spectra and the other three are single mass spectra. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window.\n+- (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately. \n+- (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra. \n+- (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra. \n+- (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups. \n+\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n+\n'

diff -r 000000000000 -r 5f18275c250a 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 01:07:13 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 5f18275c250a test-data/112_auto_combined.RData

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

diff -r 000000000000 -r 5f18275c250a test-data/112_auto_combined_QC.pdf

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

diff -r 000000000000 -r 5f18275c250a test-data/123_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.tabular Mon Oct 01 01:07:13 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 5f18275c250a 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 01:07:13 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

diff -r 000000000000 -r 5f18275c250a test-data/123_combined.RData

Binary file test-data/123_combined.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/123_combined_QC.pdf

Binary file test-data/123_combined_QC.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/12_annotation_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12_annotation_output.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+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
+7 1 msidata_2.RData file_two col2 NA NA NA
+7 2 msidata_2.RData file_two col2 NA NA NA
+7 3 msidata_2.RData file_two col2 NA NA NA
+8 1 msidata_2.RData file_two col3 NA NA NA
+8 2 msidata_2.RData file_two col3 NA NA NA
+8 3 msidata_2.RData file_two col3 NA NA NA

diff -r 000000000000 -r 5f18275c250a test-data/12_combined.RData

Binary file test-data/12_combined.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/12_combined_QC.pdf

Binary file test-data/12_combined_QC.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/2123_annotation_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2123_annotation_output.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,19 @@
+x y sample_name
+1 1 msidata_2.RData
+2 1 msidata_2.RData
+1 2 msidata_2.RData
+2 2 msidata_2.RData
+1 3 msidata_2.RData
+2 3 msidata_2.RData
+8 1 123_combined.RData
+8 2 123_combined.RData
+8 3 123_combined.RData
+10 1 123_combined.RData
+11 1 123_combined.RData
+10 2 123_combined.RData
+11 2 123_combined.RData
+10 3 123_combined.RData
+11 3 123_combined.RData
+16 1 123_combined.RData
+16 2 123_combined.RData
+16 3 123_combined.RData

diff -r 000000000000 -r 5f18275c250a test-data/2123_auto_combined.RData

Binary file test-data/2123_auto_combined.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/2123_auto_combined_QC.pdf

Binary file test-data/2123_auto_combined_QC.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/3_files_combined.RData

Binary file test-data/3_files_combined.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/Analyze75.hdr

Binary file test-data/Analyze75.hdr has changed

diff -r 000000000000 -r 5f18275c250a test-data/Analyze75.img

Binary file test-data/Analyze75.img has changed

diff -r 000000000000 -r 5f18275c250a test-data/Analyze75.t2m

Binary file test-data/Analyze75.t2m has changed

diff -r 000000000000 -r 5f18275c250a test-data/Example_Continuous.ibd

Binary file test-data/Example_Continuous.ibd has changed

diff -r 000000000000 -r 5f18275c250a test-data/Example_Continuous.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Continuous.imzML Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{51BB7C6F-9974-4626-B35F-5B65547BAE6B}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="26C26A63DCF7CD1AD768A67AEDB7131C5D88C397" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'"1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33588" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="38384" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="43180" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'

diff -r 000000000000 -r 5f18275c250a test-data/Example_Processed.ibd

Binary file test-data/Example_Processed.ibd has changed

diff -r 000000000000 -r 5f18275c250a test-data/Example_Processed.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Processed.imzML Mon Oct 01 01:07:13 2018 -0400

[

b'@@ -0,0 +1,373 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\r\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd" version="1.1">\r\n+ <cvList count="3">\r\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>\r\n+ <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\r\n+ <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\r\n+ </cvList>\r\n+ <fileDescription>\r\n+ <fileContent>\r\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{9D501BDC-5344-4916-B7E9-7E795B02C856}"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7E8FDB93053915D3EDB51B70AA0619AC209964DF"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value=""/>\r\n+ </fileContent>\r\n+ <sourceFileList count="1">\r\n+ <sourceFile id="sf1" name="Example.raw" location="C:\\Users\\Thorsten Schramm\\Documents\\Promotion\\imzML\\Website\\files\\Beispiel-Dateien\\Example images\\">\r\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>\r\n+ </sourceFile>\r\n+ </sourceFileList>\r\n+ <contact>\r\n+ <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut f\xfcr Anorganische und Analytische Chemie"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra\xdfe 60, Haus 16, Gie\xdfen, Germany"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>\r\n+ </contact>\r\n+ </fileDescription>\r\n+ <referenceableParamGroupList count="4">\r\n+ <referenceableParamGroup id="mzArray">\r\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n+ </referenceableParamGroup>\r\n+ <referenceableParamGroup id="intensityArray">\r\n+ <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n+ </referenceableParamGroup>\r\n+ <referenceableParamGroup id="scan1">\r\n+ <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>\r\n+ </referenceableParamGroup>\r\n+ <referenceableParamGroup id="spectrum1">\r\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>\r\n+ <cvParam cvRef="MS" accession="'..b'3168"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ <binaryDataArray encodedLength="0">\r\n+ <referenceableParamGroupRef ref="intensityArray"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ </binaryDataArrayList>\r\n+ </spectrum>\r\n+ <spectrum id="Scan=8" defaultArrayLength="0" index="7">\r\n+ <referenceableParamGroupRef ref="spectrum1"/>\r\n+ <scanList count="1">\r\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\r\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\r\n+ <referenceableParamGroupRef ref="scan1"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\r\n+ </scan>\r\n+ </scanList>\r\n+ <binaryDataArrayList count="2">\r\n+ <binaryDataArray encodedLength="0">\r\n+ <referenceableParamGroupRef ref="mzArray"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ <binaryDataArray encodedLength="0">\r\n+ <referenceableParamGroupRef ref="intensityArray"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ </binaryDataArrayList>\r\n+ </spectrum>\r\n+ <spectrum id="Scan=9" defaultArrayLength="0" index="8">\r\n+ <referenceableParamGroupRef ref="spectrum1"/>\r\n+ <scanList count="1">\r\n+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\r\n+ <scan instrumentConfigurationRef="LTQFTUltra0">\r\n+ <referenceableParamGroupRef ref="scan1"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\r\n+ </scan>\r\n+ </scanList>\r\n+ <binaryDataArrayList count="2">\r\n+ <binaryDataArray encodedLength="0">\r\n+ <referenceableParamGroupRef ref="mzArray"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ <binaryDataArray encodedLength="0">\r\n+ <referenceableParamGroupRef ref="intensityArray"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>\r\n+ <binary/>\r\n+ </binaryDataArray>\r\n+ </binaryDataArrayList>\r\n+ </spectrum>\r\n+ </spectrumList>\r\n+ </run>\r\n+</mzML>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 5f18275c250a test-data/Heatmaps_LM8_file16.pdf

Binary file test-data/Heatmaps_LM8_file16.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Heatmaps_analyze75.pdf

Binary file test-data/Heatmaps_analyze75.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Heatmaps_imzml.pdf

Binary file test-data/Heatmaps_imzml.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Heatmaps_rdata.pdf

Binary file test-data/Heatmaps_rdata.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Plot_analyze75.pdf

Binary file test-data/Plot_analyze75.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Plot_analyze75_allpixels.pdf

Binary file test-data/Plot_analyze75_allpixels.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Plot_empty_spectra.pdf

Binary file test-data/Plot_empty_spectra.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Plot_imzml.pdf

Binary file test-data/Plot_imzml.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/Plot_rdata.pdf

Binary file test-data/Plot_rdata.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/QC_analyze75.pdf

Binary file test-data/QC_analyze75.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/QC_empty_spectra.pdf

Binary file test-data/QC_empty_spectra.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/QC_imzml.pdf

Binary file test-data/QC_imzml.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/QC_rdata.pdf

Binary file test-data/QC_rdata.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze75.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/analyze75.svg Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="216pt" height="216pt" viewBox="0 0 216 216" version="1.1">
+<g id="surface1">
+<rect x="0" y="0" width="216" height="216" style="fill:rgb(100%,100%,100%);fill-opacity:1;stroke:none;"/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,80%);fill-opacity:1;" d="M 0 0 L 72 0 L 72 72 L 0 72 Z M 0 0 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,100%,32.156863%);fill-opacity:1;" d="M 0 72 L 72 72 L 72 144 L 0 144 Z M 0 72 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(100%,3.921569%,0%);fill-opacity:1;" d="M 0 144 L 72 144 L 72 216 L 0 216 Z M 0 144 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0%,0%);fill-opacity:1;" d="M 72 0 L 144 0 L 144 72 L 72 72 Z M 72 0 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.392157%,33.333333%);fill-opacity:1;" d="M 72 72 L 144 72 L 144 144 L 72 144 Z M 72 72 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,93.72549%);fill-opacity:1;" d="M 72 144 L 144 144 L 144 216 L 72 216 Z M 72 144 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,0.784314%,54.509804%);fill-opacity:1;" d="M 144 0 L 216 0 L 216 72 L 144 72 Z M 144 0 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.568627%,81.568627%);fill-opacity:1;" d="M 144 72 L 216 72 L 216 144 L 144 144 Z M 144 72 "/>
+<path style=" stroke:none;fill-rule:nonzero;fill:rgb(0%,1.960784%,100%);fill-opacity:1;" d="M 144 144 L 216 144 L 216 216 L 144 216 Z M 144 144 "/>
+</g>
+</svg>

diff -r 000000000000 -r 5f18275c250a test-data/analyze75_filtered2.pdf

Binary file test-data/analyze75_filtered2.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze_filtered.RData

Binary file test-data/analyze_filtered.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze_filtered.pdf

Binary file test-data/analyze_filtered.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze_filteredoutside.RData

Binary file test-data/analyze_filteredoutside.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze_originaloutput.RData

Binary file test-data/analyze_originaloutput.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/analyze_originaloutput2.RData

Binary file test-data/analyze_originaloutput2.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/annotations.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+X Y file_name column_name
+1 1 file_one col1
+1 2 file_one col1
+1 3 file_one col1
+2 1 file_one col2
+2 2 file_one col2
+2 3 file_one col2
+3 1 file_one col3
+3 2 file_one col3
+3 3 file_one col3

diff -r 000000000000 -r 5f18275c250a test-data/annotations_file1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file1.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+x y file_name column_name
+1 1 file_one col1
+1 2 file_one col1
+1 3 file_one col1
+2 1 file_one col2
+2 2 file_one col2
+2 3 file_one col2
+3 1 file_one col3
+3 2 file_one col3
+3 3 file_one col3

diff -r 000000000000 -r 5f18275c250a test-data/annotations_file2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file2.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+X Y file_name column_name
+1 1 file_two col1
+1 2 file_two col1
+1 3 file_two col1
+2 1 file_two col2
+2 2 file_two col2
+2 3 file_two col2
+3 1 file_two col3
+3 2 file_two col3
+3 3 file_two col3

diff -r 000000000000 -r 5f18275c250a test-data/annotations_file3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file3.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+X Y file_name column_name
+1 1 file_three col1
+1 2 file_three col1
+1 3 file_three col1
+2 1 file_three col2
+2 2 file_three col2
+2 3 file_three col2
+3 1 file_three col3
+3 2 file_three col3
+3 3 file_three col3

diff -r 000000000000 -r 5f18275c250a test-data/annotations_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_rdata.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,13 @@
+1 2 column_name
+1 1 column1
+1 2 column1
+1 3 column1
+3 1 column2
+3 2 column2
+3 3 column2
+4 1 column3
+4 2 column3
+4 3 column3
+9 1 column4
+9 2 column4
+9 3 column4

diff -r 000000000000 -r 5f18275c250a test-data/centroids_rdata.pdf

Binary file test-data/centroids_rdata.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/classes_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/classes_ssc.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+pixel names x y r = 1, k = 3, s = 2 r = 2, k = 3, s = 2
+xy_1_1 1 1 1 1
+xy_2_1 2 1 2 2
+xy_3_1 3 1 2 2
+xy_1_2 1 2 2 2
+xy_2_2 2 2 2 2
+xy_3_2 3 2 2 3
+xy_1_3 1 3 2 2
+xy_2_3 2 3 2 3
+xy_3_3 3 3 2 2

diff -r 000000000000 -r 5f18275c250a test-data/cluster_skm.RData

Binary file test-data/cluster_skm.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/cluster_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster_skm.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,10 @@
+pixel names x y r = 1, k = 2 r = 1, k = 3 r = 2, k = 2 r = 2, k = 3 r = 3, k = 2 r = 3, k = 3
+xy_1_1 1 1 1 1 1 1 1 3
+xy_2_1 2 1 2 2 2 2 2 2
+xy_3_1 3 1 2 3 1 3 1 3
+xy_1_2 1 2 1 1 1 1 1 3
+xy_2_2 2 2 2 2 2 2 2 2
+xy_3_2 3 2 2 3 1 3 1 3
+xy_1_3 1 3 1 1 1 1 1 1
+xy_2_3 2 3 2 2 2 2 2 2
+xy_3_3 3 3 2 3 1 3 1 3

diff -r 000000000000 -r 5f18275c250a test-data/empty_spectra.rdata

Binary file test-data/empty_spectra.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/features_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out1.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,1200 @@\n+mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n+mz_300.08\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n+mz_300.17\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n+mz_300.25\t300.25\t1.77280128848483e-10\t0\t5.31840386545449e-10\t300\t1.59552115963635e-09\t1\n+mz_300.33\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n+mz_300.42\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n+mz_300.5\t300.5\t5.50704215937811e-06\t0\t1.65211264781343e-05\t300\t4.9563379434403e-05\t1\n+mz_300.58\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n+mz_300.67\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n+mz_300.75\t300.75\t1.30250899042089e-14\t0\t3.90752697126268e-14\t300\t1.1722580913788e-13\t1\n+mz_300.83\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n+mz_300.92\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n+mz_301\t301\t0\t0\t0\tNA\t0\t0\n+mz_301.08\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n+mz_301.17\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n+mz_301.25\t301.25\t1.04927193477088e-11\t0\t3.14781580431263e-11\t300\t9.4434474129379e-11\t1\n+mz_301.33\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n+mz_301.42\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n+mz_301.5\t301.5\t1.36295095239794e-20\t0\t4.08885285719383e-20\t300\t1.22665585715815e-19\t1\n+mz_301.58\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n+mz_301.67\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n+mz_301.75\t301.75\t2.98124144276739e-15\t0\t8.94372432830217e-15\t300\t2.68311729849065e-14\t1\n+mz_301.83\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n+mz_301.92\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n+mz_302\t302\t4.80219917504923e-24\t0\t1.44065975251477e-23\t300\t4.32197925754431e-23\t1\n+mz_302.08\t302.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_302.17\t302.166687011719\t1.99229097511357e-18\t0\t5.97687292534071e-18\t300\t1.79306187760221e-17\t1\n+mz_302.25\t302.25\t5.44512547500737e-19\t0\t1.63353764250221e-18\t300\t4.90061292750663e-18\t1\n+mz_302.33\t302.333343505859\t3.63632770555763e-20\t0\t1.09089828246395e-19\t299.999991969003\t3.27269493500187e-19\t2\n+mz_302.42\t302.416687011719\t3.84359191432166e-27\t0\t1.1530775742965e-26\t300\t3.45923272288949e-26\t1\n+mz_302.5\t302.5\t9.40271183279141e-28\t0\t2.82081354983742e-27\t300\t8.46244064951227e-27\t1\n+mz_302.58\t302.583343505859\t4.19068660396836e-29\t0\t1.25720598119051e-28\t300\t3.77161794357152e-28\t1\n+mz_302.67\t302.666687011719\t0.00150662205285496\t0\t0.00451986615856489\t300\t0.0135595984756947\t2\n+mz_302.75\t302.75\t0.0266792873541514\t0\t0.0800378620624542\t300\t0.240113586187363\t2\n+mz_302.83\t302.833343505859\t0.0301816893948449\t0\t0.0905450681845347\t300\t0.271635204553604\t2\n+mz_302.92\t302.916687011719\t0.0074387863278389\t0\t0.0223163589835167\t300\t0.0669490769505501\t2\n+mz_303\t303\t0.000343241521881686\t0\t0.00102972456564506\t300\t0.00308917369693518\t2\n+mz_303.08\t303.083343505859\t1.90888501507935e-32\t0\t5.72665504523804e-32\t300\t1.71799651357141e-31\t1\n+mz_303.17\t303.166687011719\t9.50172003937247e-28\t0\t2.85051601181174e-27\t300\t8.55154803543523e-27\t1\n+mz_303.25\t303.25\t9.25846532935131e-27\t0\t2.77753959880539e-26\t300\t8.33261879641618e-26\t1\n+mz_303.33\t303.333343505859\t2.64138078718032e-06\t0\t7.92414236154097e-06\t300\t2.37724270846229e-05\t2\n+mz_303.42\t303.416687011719\t1.12685888274831e-06\t0\t3.38057664824494e-06\t300\t1.01417299447348e-05\t3\n+mz_303.5\t303.5\t1.5199399664804e-07\t0\t4.55981989944121e-07\t300\t1.36794596983236e-06\t2\n+mz_303.58\t303.583343505859\t3.97451655089665e-36\t0\t1.'..b'999999999321\t3.08614328537525e-10\t3\n+mz_396.42\t396.416687011719\t2.30604867764837e-12\t0\t6.91814603288692e-12\t299.999999997477\t2.07544380988353e-11\t3\n+mz_396.5\t396.5\t4.06171644194714e-06\t0\t1.21851492883764e-05\t299.999999077607\t3.65554479775242e-05\t4\n+mz_396.58\t396.583343505859\t1.28880310833658e-06\t0\t3.86640931417449e-06\t299.999999159279\t1.15992279750292e-05\t2\n+mz_396.67\t396.666687011719\t1.19932843361377e-07\t0\t3.5979852924763e-07\t299.999999302525\t1.0793955902524e-06\t2\n+mz_396.75\t396.75\t9.85288224826943e-15\t0\t2.95586467448083e-14\t300\t8.86759402344249e-14\t1\n+mz_396.83\t396.833343505859\t4.96342371199506e-15\t0\t1.48902711359651e-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 5f18275c250a test-data/features_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out3.tabular Mon Oct 01 01:07:13 2018 -0400

diff -r 000000000000 -r 5f18275c250a test-data/features_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test2.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,101 @@\n+mz\tncomp\tcolumn\tcoefficients\tloadings\tweights\n+938.823120117188\t2\tA\t0.00557062672565914\t0.0521481794011343\t0.0618954239030616\n+938.859741210938\t2\tA\t0.00542130109915229\t0.0573197814782043\t0.0556644462038001\n+952.817016601562\t2\tA\t0.00540658997062797\t0.0541785607809472\t0.0556957101293819\n+980.9658203125\t2\tA\t0.00530572666388636\t0.0640830071706491\t0.0596133867741965\n+948.876525878906\t2\tA\t0.00513396526933383\t0.0580901569940297\t0.0501389238916535\n+926.022705078125\t2\tA\t0.00495042111443777\t0.0562851962915777\t0.0443394574239625\n+964.835876464844\t2\tA\t0.00488062440395858\t0.0565204963990886\t0.0549598184884737\n+982.013427734375\t2\tA\t0.00485621047514792\t0.048802383602383\t0.0509744856714613\n+995.19384765625\t2\tA\t0.00481790774594767\t0.0605795860610914\t0.0530033855827968\n+980.591796875\t2\tA\t0.00471855619365328\t0.0571816843146788\t0.0534415807414751\n+907.976257324219\t2\tA\t0.00469109890013257\t0.0610286466128535\t0.0524345088122848\n+907.0048828125\t2\tA\t0.0046524995163741\t0.0496389045323984\t0.0487703720171644\n+950.238220214844\t2\tC\t0.00463861915222127\t-0.0340558630529817\t-0.0306112282051999\n+995.985229492188\t2\tA\t0.00462557611263778\t0.0467967955160554\t0.0558164362558804\n+921.521667480469\t2\tA\t0.00462412758928141\t0.0492116848139342\t0.0499849768568264\n+915.04345703125\t2\tA\t0.00454006262432388\t0.0462339924711474\t0.0425994231878204\n+929.514953613281\t2\tA\t0.00453623375772606\t0.0563841702252104\t0.045238258655595\n+958.31787109375\t2\tA\t0.00450679164876951\t0.0459566089567639\t0.0423653141505111\n+962.870727539062\t2\tC\t0.00448138616027361\t-0.0581767564414316\t-0.0599267135196269\n+942.412719726562\t2\tA\t0.00446754249696574\t0.0526251413421558\t0.0499585152758468\n+922.065551757812\t2\tA\t0.00446641275611493\t0.0495906378625035\t0.049953814799021\n+918.261596679688\t2\tC\t0.00445234724107087\t-0.0158931585724287\t-0.014157529428659\n+973.64794921875\t2\tA\t0.00445110339749622\t0.0395696753622873\t0.0372883597985613\n+991.993957519531\t2\tA\t0.00443336829341509\t0.0440255653751743\t0.0502927465261473\n+976.332946777344\t2\tA\t0.00437993281099959\t0.0492604074600163\t0.0448822073186939\n+979.582275390625\t2\tC\t0.00437918390295013\t-0.0344798097888197\t-0.03253979930277\n+913.41845703125\t2\tC\t0.00437503486499096\t-0.00387925008074657\t-0.00438981731141592\n+948.619018554688\t2\tA\t0.00426105794044819\t0.0371821841057357\t0.0429237139078889\n+901.330810546875\t2\tA\t0.00425328221665412\t0.0552699147993945\t0.0482509891289382\n+960.278381347656\t2\tC\t0.00423132265179973\t-0.0433340796542259\t-0.0409361343266309\n+992.294921875\t2\tC\t0.00418576359850056\t-0.0391910598190591\t-0.0342798229241432\n+994.967834472656\t2\tA\t0.00417817188823829\t0.0383119007479891\t0.0476486709797929\n+948.471862792969\t2\tA\t0.00417161016294321\t0.0380099525316105\t0.0408760564074696\n+904.237426757812\t2\tA\t0.00417080429266561\t0.0475165460962433\t0.0430960180049384\n+942.852722167969\t2\tB\t0.0041438458930486\t-0.0468558588772594\t-0.049716939342293\n+918.442565917969\t2\tA\t0.00413331124379944\t0.0423300908408027\t0.0458013372312651\n+943.109436035156\t2\tB\t0.00412811549109012\t-0.0413767608692901\t-0.0472745376109769\n+936.5556640625\t2\tA\t0.00411371014807382\t0.0407060654246003\t0.0414790745602655\n+945.054321289062\t2\tA\t0.00408474594381495\t0.0481061599030778\t0.0422885605529943\n+992.595886230469\t2\tA\t0.00408223122742656\t0.0369204499600823\t0.0410564204257673\n+913.310180664062\t2\tA\t0.00407879803557168\t0.0498424674382356\t0.040014655663535\n+910.965698242188\t2\tC\t0.00405962992021169\t-0.0382641079076008\t-0.0379558138613928\n+950.606384277344\t2\tC\t0.00405907592689352\t-0.0503005800552258\t-0.0564684538983107\n+974.020629882812\t2\tA\t0.00404970841392063\t0.0453076176593101\t0.0358031960147686\n+903.770629882812\t2\tC\t0.00403337646658259\t-0.0308928430941287\t-0.035800455446528\n+993.197998046875\t2\tC\t0.00402476056402085\t-0.022740013818147\t-0.0229211765138961\n+955.140930175781\t2\tA\t0.00400392811033344\t0.0545303511096986\t0.0430366824723547\n+923.734497070312\t2\tA\t0.00396875769656089\t0.0489283101050371\t0.0446083164881897\n+943.292846679688\t2\tC\t0.00396229091310485\t-0.00589037926949604\t-0.0081255927937416\n+927.7680053'..b'95776036645286\t-0.0622321071450148\t-0.0629368131896196\n+907.508483886719\t2\tA\t0.00394876742672506\t0.0338904158180818\t0.0315098966370126\n+960.019287109375\t2\tA\t0.0039403473862032\t0.050776397569013\t0.03873623640836\n+925.041748046875\t2\tC\t0.0039362983069634\t0.00547894918105684\t0.00648384039698146\n+922.863586425781\t2\tA\t0.00393043741778826\t0.0404768313565869\t0.0320371152599393\n+918.985595703125\t2\tC\t0.00392990559936248\t-0.0241976051228088\t-0.0173907002587976\n+938.054809570312\t2\tA\t0.00392283092987214\t0.0433932714795145\t0.0415656785679352\n+952.300964355469\t2\tA\t0.00391807330597071\t0.0539847824089577\t0.0526900756993094\n+938.896301269531\t2\tA\t0.00390920544867313\t0.0432075299467666\t0.040884460919137\n+918.62353515625\t2\tA\t0.00390598520310851\t0.0405436877403175\t0.0394150273697351\n+940.653686523438\t2\tA\t0.00388205579523716\t0.0325670207445315\t0.0376845331490984\n+918.587341308594\t2\tA\t0.00386025843595639\t0.0420256786308284\t0.0473925689610602\n+944.063293457031\t2\tC\t0.00384447645727029\t-0.0108918102769628\t-0.00500447372654549\n+980.479553222656\t2\tC\t0.00383412917234354\t-0.0262635632207469\t-0.0305873497852977\n+905.854248046875\t2\tC\t0.00382809625193645\t-0.0509229481136295\t-0.0545129795504416\n+942.082763671875\t2\tA\t0.00381273797189762\t0.0444743475872274\t0.0435604050553623\n+934.656066894531\t2\tC\t0.00378297587449155\t-0.0394312931297934\t-0.0485932573378814\n+906.89697265625\t2\tA\t0.00374570932202412\t0.0339271553171168\t0.0282809191934174\n+905.890197753906\t2\tC\t0.00373151556865197\t-0.024218298123225\t-0.0186657492773445\n+948.655822753906\t2\tC\t0.00372441631900937\t-0.017476081747813\t-0.0110316891494553\n+959.908325195312\t2\tA\t0.00371442848581406\t0.0342932290876843\t0.0310906799107696\n+946.192810058594\t2\tB\t0.00369361746355479\t-0.038238592789904\t-0.0417491451554952\n+933.524536132812\t2\tA\t0.00368140176962546\t0.0376205271222568\t0.0348149137052689\n+999.531311035156\t2\tA\t0.0036708372022316\t0.0419178472824249\t0.0360426545514402\n+905.602661132812\t2\tA\t0.00366188804899887\t0.0371789230194049\t0.0403042300562272\n+904.560729980469\t2\tA\t0.00366151022492225\t0.0483872255903629\t0.0393416043647449\n+967.02587890625\t2\tA\t0.00364664009773375\t0.0358270208382791\t0.0367448112342897\n+961.833374023438\t2\tA\t0.00364124181915343\t0.0500921543232852\t0.0471568448381178\n+945.71533203125\t2\tA\t0.00362363829859195\t0.038772747366622\t0.038929243234765\n+994.026245117188\t2\tB\t0.00362302096270583\t-0.0278102959641648\t-0.035044986078868\n+922.138061523438\t2\tA\t0.0036165759251259\t0.0396894571745094\t0.0338599942728403\n+921.920471191406\t2\tC\t0.00361497501678999\t-0.0109725715482311\t-0.00817330765900041\n+996.512939453125\t2\tC\t0.00361344604654759\t-0.0240208863758058\t-0.0216798334099216\n+925.586669921875\t2\tC\t0.00360019116631399\t-0.000201285421933851\t-0.00370132703005591\n+927.076965332031\t2\tA\t0.00359739327950109\t0.0402217752115896\t0.0381187534803433\n+946.266296386719\t2\tA\t0.00359027149639919\t0.0350158580852316\t0.0345803953604497\n+997.644348144531\t2\tC\t0.00358755032912394\t-0.0386413413940509\t-0.0374227165960138\n+986.959838867188\t2\tC\t0.00356886986009821\t-0.00770354721402719\t-0.0073488017929185\n+956.544067382812\t2\tB\t0.00356755616082941\t-0.0263554430477736\t-0.0341563371597065\n+981.826293945312\t2\tA\t0.0035614851177778\t0.0318618564397332\t0.0359368988957353\n+995.683715820312\t2\tA\t0.0035606803581847\t0.0326251406575274\t0.0326734264590619\n+949.575622558594\t2\tA\t0.00354754516564472\t0.0399068842159591\t0.0381317579086198\n+990.565063476562\t2\tC\t0.00354075441437422\t-0.00252469837204454\t-0.00790021238532976\n+970.222473144531\t2\tA\t0.00353702890647679\t0.033894961483528\t0.0342653656238723\n+926.277160644531\t2\tC\t0.00352995388417487\t-0.00403664201467942\t-0.00483641570245392\n+981.15283203125\t2\tA\t0.00352226894457903\t0.0343450789571067\t0.0416777456263345\n+927.222412109375\t2\tA\t0.00350510856591621\t0.0346202558912905\t0.033535024774141\n+946.450012207031\t2\tA\t0.00349425060263787\t0.0428865972028226\t0.0325784624960938\n+979.395385742188\t2\tC\t0.00349405845239093\t-0.00985834384583178\t-0.00848238004662365\n+902.083984375\t2\tA\t0.00349155533954646\t0.0283241643148307\t0.0297190584575691\n'

diff -r 000000000000 -r 5f18275c250a test-data/features_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test4.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,101 @@\n+mz\tncomp\tcolumn\tcoefficients\tloadings\tweights\n+912.877136230469\t3\tB\t0.00402511569666969\t-0.246308032464734\t-0.0998747661753797\n+928.8232421875\t3\tA\t0.00355204006388532\t0.273286934815558\t0.288081987978036\n+928.859680175781\t3\tB\t0.00304099166534859\t-0.180023925015396\t-0.0975882865489913\n+929.806274414062\t3\tA\t0.00301867966492034\t0.20461792386307\t0.204104875190971\n+928.786865234375\t3\tA\t0.00294246516676733\t0.279365597419633\t0.24012019090174\n+912.913208007812\t3\tB\t0.00221421341476842\t-0.25734495461644\t-0.123924205177262\n+906.357543945312\t3\tB\t0.0017751956946221\t0.0660711931225974\t-0.167734534471784\n+913.887756347656\t3\tB\t0.00169164545723661\t-0.0797847981582402\t-0.0542158398194389\n+907.400573730469\t3\tA\t0.00168976824209188\t-0.0553409573032757\t-0.0310185392575794\n+900.3271484375\t3\tA\t0.0016850771109767\t0.0635456830152988\t0.0623351620915374\n+928.896057128906\t3\tB\t0.00168450000766379\t-0.182486440635111\t-0.0950023449824687\n+922.355712890625\t3\tA\t0.00167096941795371\t0.0529977859368994\t0.0679949938623556\n+900.398864746094\t3\tA\t0.00166100096018687\t0.0406827592981194\t-0.010027514312194\n+960.315368652344\t3\tA\t0.00164686513200881\t0.0692239228029656\t0.0559857485267436\n+964.353698730469\t3\tA\t0.0016007991522707\t0.0487859885763137\t0.049315043939497\n+906.3935546875\t3\tA\t0.00157421991835154\t-0.184824638462265\t-0.161519730620847\n+964.316589355469\t3\tA\t0.00143180642589214\t0.0309764043652652\t0.0453653991628429\n+962.31494140625\t3\tA\t0.00141328760599612\t0.0642563963154312\t0.0454439922528048\n+929.879089355469\t3\tB\t0.00137108902531006\t-0.147152863346693\t-0.0787919913569194\n+900.434692382812\t3\tB\t0.00131488882358473\t-0.20214180256976\t-0.173026933354479\n+901.402526855469\t3\tA\t0.00131071912036092\t0.0193425453272541\t0.00416556425120399\n+922.391967773438\t3\tA\t0.00128195781418033\t0.0250080230991378\t0.0401690309084914\n+915.33251953125\t3\tA\t0.00127720082168308\t0.0472700250545067\t0.0476142683041524\n+938.310852050781\t3\tA\t0.00126979651175339\t0.0258332330864995\t0.0395551945184375\n+913.923889160156\t3\tB\t0.00125913909333928\t-0.116366449217641\t-0.0823808975691949\n+907.508483886719\t3\tA\t0.00123463128203684\t0.0286834379044553\t0.0416260189187914\n+974.356140136719\t3\tA\t0.00122974867070485\t0.0426004370460666\t0.0327898050985416\n+933.451599121094\t3\tA\t0.00122075781571264\t0.0189293266454833\t0.0363946273679358\n+910.352966308594\t3\tA\t0.00121465945239948\t0.0212318588989688\t0.0191774558940735\n+990.339538574219\t3\tA\t0.00120033930835288\t0.0471035220902788\t0.0441020126132822\n+984.41015625\t3\tA\t0.00117709585424916\t0.0256612782877473\t0.0364785894847815\n+922.319458007812\t3\tA\t0.00116343926435404\t0.0350575504771194\t0.049003566656031\n+945.825500488281\t3\tA\t0.00116281366134625\t0.0358386234196617\t0.039941557361758\n+914.429443359375\t3\tA\t0.00114751581370748\t0.0214325420152595\t0.0322577162355903\n+934.364013671875\t3\tA\t0.00111966105461266\t0.0261184955739278\t0.0277902861913678\n+945.788757324219\t3\tA\t0.0011140971316516\t0.0602657244502292\t0.0678490003014779\n+930.27978515625\t3\tA\t0.00111107830564362\t0.0548573050563774\t0.0541864639681832\n+987.41015625\t3\tA\t0.00109109627880292\t0.0259022291567729\t0.0348827329301489\n+917.320922851562\t3\tB\t0.00108811988692458\t-0.0380939775497376\t-0.0859734761406655\n+961.388977050781\t3\tA\t0.00108270610537361\t0.0208991144261707\t0.0235951714502884\n+949.244445800781\t3\tA\t0.00108094226185502\t0.0553461544724562\t0.0473287208302763\n+914.393310546875\t3\tA\t0.00107937289161071\t0.0186407876697643\t0.0213451871968151\n+923.37158203125\t3\tA\t0.00107406087109902\t0.0174157121297602\t0.0300927241546599\n+967.322998046875\t3\tA\t0.00106160501633174\t0.0413827618597132\t0.0291509896006055\n+961.314880371094\t3\tA\t0.00105652394646208\t0.0429555520663857\t0.0345573512639803\n+994.252197265625\t3\tA\t0.00105259315733988\t0.0465400676246555\t0.0444177569572566\n+945.348083496094\t3\tA\t0.00104820825219221\t0.00490478080758506\t0.00553720261210505\n+913.346313476562\t3\tA\t0.00103460925930171\t0.0189564108870971\t0.026732642281156\n+914.321105957031\t3\tA\t0.00103017762730726\t0.0282931942786005\t0.0284256699648362\n+929.442138671875\t3\tA\t0.001024049715'..b'65625\t3\tA\t0.0010201655110503\t0.00439147989742666\t0.022483171550914\n+978.386474609375\t3\tA\t0.00101071432463861\t0.0477124446667881\t0.0315232247977375\n+939.335510253906\t3\tA\t0.00100997005380696\t0.0115288494115123\t0.0213424433245233\n+929.478515625\t3\tA\t0.00100973338976312\t0.0376043223441187\t0.0393591980443549\n+939.079284667969\t3\tA\t0.00100844892647231\t0.031219827705917\t0.0442017366717789\n+943.843139648438\t3\tA\t0.000998522723296839\t0.0267299053728509\t0.036566368840497\n+929.842712402344\t3\tA\t0.000985861500832982\t0.0831947546006432\t0.10803783679681\n+940.397277832031\t3\tA\t0.000981083898431389\t0.0151431322576335\t0.0277538495060947\n+990.302001953125\t3\tA\t0.000975080019411607\t0.0394636635241222\t0.0357960840702764\n+913.310180664062\t3\tA\t0.000968769911918236\t0.0107823038071007\t0.0262423379384436\n+912.3359375\t3\tA\t0.000967109425146236\t0.0334299345844847\t0.0262269905676808\n+934.327514648438\t3\tA\t0.000965358942233967\t0.0380560763121743\t0.0247830327164836\n+978.34912109375\t3\tA\t0.000951696141507144\t0.0246378024631849\t0.0263610910562008\n+964.427856445312\t3\tA\t0.000949632779126584\t0.0206276476766682\t0.0323633524966416\n+905.135498046875\t3\tA\t0.000938890795440174\t0.0358363374682948\t0.0462758721204666\n+902.9091796875\t3\tA\t0.000928200839226985\t0.0270476983876206\t0.0331256977422899\n+970.296875\t3\tA\t0.000917937154598045\t0.0412888009110875\t0.0371046212107984\n+900.291320800781\t3\tA\t0.000915554291393151\t0.036900837325731\t0.0299428712446064\n+936.372924804688\t3\tA\t0.00091425261278822\t0.0304697260564217\t0.0172307486843934\n+902.550354003906\t3\tA\t0.000913173677427114\t0.0206873082762993\t0.0314356257688807\n+969.329895019531\t3\tA\t0.00090861890412644\t0.0381404597757337\t0.0290496620448507\n+928.350158691406\t3\tB\t0.000900790180107579\t-0.0354285882483893\t-0.0781235087794192\n+906.465454101562\t3\tA\t0.000894886810510601\t0.0278152115913203\t0.00415630972695765\n+951.195617675781\t3\tA\t0.00088960840060638\t0.0213781455200748\t0.0390510024922428\n+929.296508789062\t3\tA\t0.00088945452659998\t0.0574166486840185\t0.0407909727744226\n+910.389038085938\t3\tA\t0.000888660624855818\t0.00883285913101179\t0.024080334566073\n+900.362976074219\t3\tA\t0.000883637632569096\t0.0601212422828572\t0.020862039569661\n+938.274291992188\t3\tA\t0.000883070665782107\t0.0420871600944523\t0.0280462808036272\n+978.423828125\t3\tA\t0.000872970230052765\t0.0296257238522422\t0.0297815743118744\n+911.326171875\t3\tA\t0.00086789849916482\t0.0394187876318227\t0.0290756595311376\n+931.700927734375\t3\tA\t0.000861266010686886\t0.0280254327018276\t0.0337516683459626\n+974.393371582031\t3\tA\t0.00086077059179462\t0.0419836959861716\t0.0289479495170414\n+948.251220703125\t3\tA\t0.000851477547904384\t0.0586205266644055\t0.0458040438736673\n+930.862670898438\t3\tB\t0.000847409031672241\t-0.0301586503036759\t-0.0413625782185381\n+916.923034667969\t3\tA\t0.000845064368244676\t0.0201331942543559\t0.0318311721846992\n+949.318054199219\t3\tA\t0.000844949051475147\t0.0315506908752857\t0.0279475612749433\n+985.459655761719\t3\tA\t0.000842609316199747\t0.0291683495191316\t0.0295586583634342\n+907.4365234375\t3\tA\t0.000842558751196136\t0.0249644273710741\t0.0174278577017741\n+925.18701171875\t3\tA\t0.000838340515097191\t0.0229497739599204\t0.0228814357718886\n+929.332885742188\t3\tB\t0.000836809726794182\t-0.0293672010070615\t-0.0547646716148819\n+937.506225585938\t3\tA\t0.000833507239635534\t0.0178457519825421\t0.0278222013471842\n+987.335083007812\t3\tA\t0.000833440336912753\t0.0308912024371622\t0.0275278913639686\n+987.372619628906\t3\tA\t0.000826015704761948\t0.0386304306725754\t0.0226104858957154\n+991.392211914062\t3\tA\t0.000822495593430933\t0.0301123283528462\t0.0258405716069016\n+986.359619140625\t3\tA\t0.00081725052418651\t0.0222459076819841\t0.0214131889306635\n+995.608337402344\t3\tA\t0.000815403977582455\t0.0244745957678714\t0.0372521871817605\n+901.438415527344\t3\tB\t0.000811802591576616\t-0.14481476191689\t-0.105509238222151\n+927.295166015625\t3\tA\t0.000809570499146196\t0.0324202661433909\t0.0195781537578164\n+957.467712402344\t3\tA\t0.000805168267772138\t0.0349607008493259\t0.0294205742236357\n+982.387756347656\t3\tA\t0.000802321450704626\t0.0296134673806074\t0.0240390222467118\n'

diff -r 000000000000 -r 5f18275c250a test-data/features_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test6.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,21 @@
+mz r k s classes centers tstatistics p.values adj.p.values
+928.859680175781 2 3 2 B 43.9516959905118 0.541814677313986 0.607464263577403 1
+912.877136230469 2 3 2 B 55.419364071664 0.437808238568372 0.676846169835776 1
+913.887756347656 2 3 2 B 24.9140214890445 0.393340199810185 0.70766449744142 1
+930.862670898438 2 3 2 B 9.28583084091344 0.29858210475084 0.775329712997245 1
+913.923889160156 2 3 2 B 12.1491837287613 0.0960056413112618 0.926642424678888 1
+900.004699707031 2 3 2 A 2.29166666666667 0 1 1
+900.04052734375 2 3 2 A 3.125 0 1 1
+900.076354980469 2 3 2 A 3.33333333333333 0 1 1
+900.112182617188 2 3 2 A 3.45833333333333 0 1 1
+900.148010253906 2 3 2 A 3.29166666666667 0 1 1
+900.183837890625 2 3 2 A 3.375 0 1 1
+900.219665527344 2 3 2 A 3.66666666666667 0 1 1
+900.255493164062 2 3 2 A 3.91666666666667 0 1 1
+900.291320800781 2 3 2 A 4.08333333333333 0 1 1
+900.3271484375 2 3 2 A 5.79166666666667 0 1 1
+900.362976074219 2 3 2 A 11.5416666666667 0 1 1
+900.398864746094 2 3 2 A 26.2083333333333 0 1 1
+900.434692382812 2 3 2 A 30.0416666666667 0 1 1
+900.470520019531 2 3 2 A 19.1666666666667 0 1 1
+900.50634765625 2 3 2 A 8.5 0 1 1

diff -r 000000000000 -r 5f18275c250a test-data/features_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test7.tabular Mon Oct 01 01:07:13 2018 -0400

diff -r 000000000000 -r 5f18275c250a test-data/featuresofinterest5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,31 @@
+115.333335876465
+115.416664123535
+115.5
+115.583335876465
+115.666664123535
+115.75
+115.833335876465
+115.916664123535
+116
+116.083335876465
+116.166664123535
+116.25
+116.333335876465
+116.416664123535
+116.5
+116.583335876465
+116.666664123535
+319.083343505859
+319.166687011719
+319.25
+319.333343505859
+319.416687011719
+319.5
+319.583343505859
+319.666687011719
+319.75
+319.8
+319.916687011719
+320
+320.0833435
+350

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered.RData

Binary file test-data/imzml_filtered.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered.pdf

Binary file test-data/imzml_filtered.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered2.pdf

Binary file test-data/imzml_filtered2.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered3.RData

Binary file test-data/imzml_filtered3.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered3.pdf

Binary file test-data/imzml_filtered3.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered4.RData

Binary file test-data/imzml_filtered4.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered4.pdf

Binary file test-data/imzml_filtered4.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered5.RData

Binary file test-data/imzml_filtered5.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/imzml_filtered5.pdf

Binary file test-data/imzml_filtered5.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/inputcalibrantfile1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,3 @@
+101.5
+356.7
+555.1

diff -r 000000000000 -r 5f18275c250a test-data/inputcalibrantfile2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,3 @@
+869.51 mass1
+1111.1 mass2
+1296.7 mass3

diff -r 000000000000 -r 5f18275c250a test-data/inputpeptides.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,3 @@
+152 mass1
+328.9 mass2
+185.2 mass3

diff -r 000000000000 -r 5f18275c250a test-data/inputpeptides2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,4 @@
+854.5
+1111.1
+1296.7
+1305.1

diff -r 000000000000 -r 5f18275c250a test-data/inputpixels_2column.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,6 @@
+1 A 1
+1 B 2
+1 C 3
+3 D 1
+3 E 2
+30 F 3

diff -r 000000000000 -r 5f18275c250a test-data/int_matrix1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix1.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,1200 @@\n+mz_name\txy_1_1\txy_2_1\txy_3_1\txy_1_2\txy_2_2\txy_3_2\txy_1_3\txy_2_3\txy_3_3\n+mz_300.08\t0\t0\t0\t0\t0.263692855834961\t0\t0\t0\t0\n+mz_300.17\t0\t0\t0\t0\t0.0258997213095427\t0\t0\t0\t0\n+mz_300.25\t0\t1.59552115963635e-09\t0\t0\t0\t0\t0\t0\t0\n+mz_300.33\t0\t4.6339512782545e-10\t0\t0\t0\t0\t0\t0\t0\n+mz_300.42\t0\t3.61252902592035e-11\t0\t0\t0\t0\t0\t0\t0\n+mz_300.5\t0\t0\t0\t0\t4.9563379434403e-05\t0\t0\t0\t0\n+mz_300.58\t0\t0\t0\t0\t3.55600786861032e-05\t0\t0\t0\t0\n+mz_300.67\t0\t0\t0\t0\t6.54657515042345e-06\t0\t0\t0\t0\n+mz_300.75\t0\t1.1722580913788e-13\t0\t0\t0\t0\t0\t0\t0\n+mz_300.83\t0\t6.54903445384582e-14\t0\t0\t0\t0\t0\t0\t0\n+mz_300.92\t0\t1.07130575705038e-14\t0\t0\t0\t0\t0\t0\t0\n+mz_301\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_301.08\t0\t0\t0\t0\t3.82026943412939e-09\t0\t0\t0\t0\n+mz_301.17\t0\t0\t0\t0\t1.14051934563264e-09\t0\t0\t0\t0\n+mz_301.25\t0\t0\t0\t0\t9.4434474129379e-11\t0\t0\t0\t0\n+mz_301.33\t0\t7.46476736089292e-18\t0\t0\t0\t0\t0\t0\t0\n+mz_301.42\t0\t1.98718499598743e-18\t0\t0\t0\t0\t0\t0\t0\n+mz_301.5\t0\t1.22665585715815e-19\t0\t0\t0\t0\t0\t0\t0\n+mz_301.58\t0\t0\t0\t0\t2.70808522091423e-13\t0\t0\t0\t0\n+mz_301.67\t0\t0\t0\t0\t1.59419406928901e-13\t0\t0\t0\t0\n+mz_301.75\t0\t0\t0\t0\t2.68311729849065e-14\t0\t0\t0\t0\n+mz_301.83\t0\t6.06203431656678e-22\t0\t0\t0\t0\t0\t0\t0\n+mz_301.92\t0\t2.91142836940678e-22\t0\t0\t0\t0\t0\t0\t0\n+mz_302\t0\t4.32197925754431e-23\t0\t0\t0\t0\t0\t0\t0\n+mz_302.08\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_302.17\t0\t0\t0\t0\t1.79306187760221e-17\t0\t0\t0\t0\n+mz_302.25\t0\t0\t0\t0\t4.90061292750663e-18\t0\t0\t0\t0\n+mz_302.33\t0\t7.7875562784001e-27\t0\t0\t3.27269485712631e-19\t0\t0\t0\t0\n+mz_302.42\t0\t3.45923272288949e-26\t0\t0\t0\t0\t0\t0\t0\n+mz_302.5\t0\t8.46244064951227e-27\t0\t0\t0\t0\t0\t0\t0\n+mz_302.58\t0\t3.77161794357152e-28\t0\t0\t0\t0\t0\t0\t0\n+mz_302.67\t0\t0\t0\t0.0135595984756947\t1.41553322001893e-21\t0\t0\t0\t0\n+mz_302.75\t0\t0\t0\t0.240113586187363\t7.10063369068687e-22\t0\t0\t0\t0\n+mz_302.83\t0\t0\t0\t0.271635204553604\t1.08665147932087e-22\t0\t0\t0\t0\n+mz_302.92\t0\t3.04753906993054e-30\t0\t0.0669490769505501\t0\t0\t0\t0\t0\n+mz_303\t0\t1.28620729883923e-30\t0\t0.00308917369693518\t0\t0\t0\t0\t0\n+mz_303.08\t0\t1.71799651357141e-31\t0\t0\t0\t0\t0\t0\t0\n+mz_303.17\t0\t0\t0\t0\t8.55154803543523e-27\t0\t0\t0\t0\n+mz_303.25\t0\t0\t0\t0\t8.33261879641618e-26\t0\t0\t0\t0\n+mz_303.33\t0\t0\t0\t2.37724270846229e-05\t2.09127303308002e-26\t0\t0\t0\t0\n+mz_303.42\t0\t9.58168691215212e-35\t0\t1.01417299447348e-05\t1.04388012620863e-27\t0\t0\t0\t0\n+mz_303.5\t0\t1.58932794058987e-34\t0\t1.36794596983236e-06\t0\t0\t0\t0\t0\n+mz_303.58\t0\t3.57706489580698e-35\t0\t0\t0\t0\t0\t0\t0\n+mz_303.67\t0\t9.35872582472049e-37\t0\t0\t0\t0\t0\t0\t0\n+mz_303.75\t0\t0\t0\t0\t7.17247682883041e-30\t0\t0\t0\t0\n+mz_303.83\t0\t0\t0\t7.12931158552976e-10\t3.14272590048273e-30\t0\t0\t0\t0.243055954575539\n+mz_303.92\t0\t0\t0\t1.24892662878295e-09\t0.0277397744357586\t0\t0\t0\t0.498759061098099\n+mz_304\t0\t1.32924944261294e-38\t0\t2.8316210487489e-10\t0.411686420440674\t0\t0\t0\t0.609295308589935\n+mz_304.08\t0.0905158519744873\t0\t0\t7.8840970210714e-12\t0.275029838085175\t0\t0\t0\t0.213168099522591\n+mz_304.17\t0.313372820615768\t0\t0\t0\t0.0508057586848736\t0\t0\t0\t0.0229585953056812\n+mz_304.25\t0.121097885072231\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_304.33\t0.013486223295331\t0\t0\t0\t0\t0\t0.00300684501416981\t0\t0\n+mz_304.42\t0\t0\t0\t1.17177887401856e-13\t0\t0\t0.16572842001915\t0\t0\n+mz_304.5\t0\t0\t0\t4.45529911249389e-14\t0\t0\t0.279548346996307\t0.00212043104693294\t0\n+mz_304.58\t0\t0\t0.302276760339737\t5.34932731113434e-15\t2.94947021757253e-05\t0\t0.0847897008061409\t0.2228934019804\t0.209528908133507\n+mz_304.67\t1.76512676262064e-05\t0\t0.478220641613007\t0\t8.835948392516e-06\t0\t0.00725169805809855\t0.456041157245636\t0.329809844493866\n+mz_304.75\t1.58223701873794e-05\t0\t0.148877888917923\t0\t7.36899835374061e-07\t0\t0\t0.131635144352913\t0.105051673948765\n+mz_304.83\t3.14090880237927e-06\t0\t0.0133870458230376\t0\t0\t0\t0\t0.0101162772625685\t0.00984159205108881\n+mz_304.92\t0\t0\t0\t5.25034571767466e-18\t0\t0\t0.0188857112079859\t0\t0\n+mz_305\t0\t0\t0\t5.69736818276873e-18\t0\t0\t0.716848015785217\t0\t0\n+mz_305.08\t0\t0\t0\t1.18824205480028e-18\t2.08106776256045e-09\t0\t0.583352088928223\t0\t0\n+mz_305.17\t0\t0\t3.19467071676627e-05\t9.44219802983962e-21\t1.23338206314827e-09\t0\t0.115305423736572\t3.37689161824528e-05\t2.12734430533601e-05\n+mz_305.25\t1.62699820283052e-09\t0\t2.04717780434294e-05\t0\t2.08315351080124e-10\t0\t0\t1.86496217793319e-05\t1.43190909511759'..b'9125789107e-10\t0.310508847236633\n+mz_394.92\t0\t0\t9.62898286324196e-18\t0\t0\t1.5011888920002e-23\t0\t0\t0.203106641769409\n+mz_395\t0\t0\t0\t0\t0\t0\t0\t0\t0.0395353808999062\n+mz_395.08\t0\t0\t0.166029959917068\t0\t0\t0\t0\t0\t0\n+mz_395.17\t0\t0\t0.23992046713829\t0\t0\t0\t0\t0\t0\n+mz_395.25\t0\t0\t0.0718047022819519\t0\t0\t8.90397842411612e-26\t0\t1.33592328822527e-13\t0\n+mz_395.33\t0\t0\t0.0059764008037746\t0\t0\t4.05360952454079e-26\t0\t3.63706189731444e-14\t0\n+mz_395.42\t0\t0\t0\t0\t0\t5.7772844691443e-27\t0\t2.40205711292169e-15\t2.11353399208747e-05\n+mz_395.5\t0\t0\t0\t0\t0\t0\t0\t0\t6.69534847475006e-06\n+mz_395.58\t0\t0\t0\t0\t0\t0\t0\t0\t6.21269464318175e-07\n+mz_395.67\t0\t0\t1.69494323927211e-05\t0\t0\t0\t0\t0\t0\n+mz_395.75\t0\t0\t1.00270171969896e-05\t0\t0\t1.85556522870521e-30\t0\t1.05916895745363e-17\t0\n+mz_395.83\t0\t0\t1.69196300703334e-06\t0.05777582898736\t0\t4.8930473332074e-30\t0\t5.27836397938306e-18\t0\n+mz_395.92\t0\t0\t0\t0.511816620826721\t0\t1.15794102281988e-30\t0\t8.04196416956264e-19\t1.37501721120259e-09\n+mz_396\t0\t0\t0\t0.35160955786705\t0\t4.33367092554234e-32\t0\t0\t9.14517350736332e-10\n+mz_396.08\t0\t0\t0\t0.0685468316078186\t0\t0\t0\t0\t1.63165772559815e-10\n+mz_396.17\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_396.25\t0\t0\t1.12639098048817e-09\t0\t0\t0\t0\t7.5080259483855e-23\t0\n+mz_396.33\t0\t0\t3.08614328536905e-10\t0\t0\t4.43552910897872e-34\t0\t6.20559538928448e-22\t0\n+mz_396.42\t0\t0\t2.07544380986802e-11\t0\t0\t1.78635181404722e-34\t0\t1.55153831792916e-22\t0\n+mz_396.5\t0\t0\t0\t3.65554478776176e-05\t0\t2.28090559069531e-35\t0\t7.62271717321813e-24\t9.99066823194339e-14\n+mz_396.58\t0\t0\t0\t1.15992279461352e-05\t0\t0\t0\t0\t2.88939709560797e-14\n+mz_396.67\t0\t0\t0\t1.07939558802173e-06\t0\t0\t0\t0\t2.23067100747309e-15\n+mz_396.75\t0\t0\t8.86759402344249e-14\t0\t0\t0\t0\t0\t0\n+mz_396.83\t0\t0\t4.46708134079019e-14\t0\t0\t1.77230652599915e-38\t0\t5.36047748391913e-26\t0\n+mz_396.92\t0\t0\t6.85586688738441e-15\t0\t0\t2.28012433765444e-38\t0\t2.33549728191425e-26\t0\n+mz_397\t0\t0\t0\t0.0388109683990479\t0\t0\t0\t3.20919536266692e-27\t7.3794850397387e-18\n+mz_397.08\t0\t0\t0\t0.288620352745056\t0\t0\t0\t0\t4.0904726491625e-18\n+mz_397.17\t0\t0\t0\t0.179139345884323\t0\t0\t0\t0\t6.66140851600565e-19\n+mz_397.25\t0\t0\t4.74347756244299e-19\t0.0324370078742504\t0\t0\t0\t0\t0\n+mz_397.33\t0\t0\t5.23588866851877e-18\t0\t0\t0\t0\t1.45252028329413e-30\t0\n+mz_397.42\t0\t0\t1.31735450526457e-18\t0\t0\t0\t0\t2.85723650272451e-30\t0\n+mz_397.5\t0\t0\t6.64366394090274e-20\t0\t0\t0\t0\t6.57045764736752e-31\t0\n+mz_397.58\t0\t0\t0\t0\t0\t0\t0\t2.04047937094937e-32\t4.67197860272674e-22\n+mz_397.67\t0\t0\t0\t1.94183921848889e-05\t0\t0\t0\t0\t1.23865323750669e-22\n+mz_397.75\t0\t0\t0\t5.69980966247385e-06\t0\t0\t0\t0\t7.54736833499504e-24\n+mz_397.83\t0\t0\t4.49627188988339e-22\t4.5503847445616e-07\t0\t0\t0\t0\t0\n+mz_397.92\t0\t0\t1.977578363903e-22\t0\t0\t0\t0\t2.65117092875872e-34\t0\n+mz_398\t0\t0\t2.73956025372824e-23\t0\t0\t0\t0\t1.02695755303769e-34\t0\n+mz_398.08\t0\t0\t0.0391987599432468\t0\t0\t0\t0\t1.25882128826124e-35\t3.81025795308296e-26\n+mz_398.17\t0\t0\t0.428542405366898\t1.40762135281136e-09\t0\t0\t0\t0\t1.81789914120271e-26\n+mz_398.25\t0\t0\t0.303975909948349\t8.02108046649153e-10\t0\t0\t0\t0\t2.6856332332152e-27\n+mz_398.33\t0\t0\t0.0511138886213303\t1.32665364804829e-10\t0\t0\t0\t0\t0\n+mz_398.42\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_398.5\t0\t0\t0\t0\t0\t0\t0\t1.30501076268597e-38\t0\n+mz_398.58\t0\t0\t0\t0\t0\t0\t0\t0\t5.28061120609724e-31\n+mz_398.67\t0\t0\t0.0123793203383684\t0.0204813592135906\t0\t0\t0\t0\t2.16410654088079e-30\n+mz_398.75\t0\t0\t0.234551697969437\t0.642472565174103\t0\t0\t0\t0\t5.27295168490728e-31\n+mz_398.83\t0\t0\t0.197811514139175\t0.546955585479736\t0\t0\t0\t0\t2.30524654303423e-32\n+mz_398.92\t0\t0\t0.0379873886704445\t0.110048480331898\t0\t0\t0\t0\t0\n+mz_399\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.08\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.17\t0\t0\t0\t0\t0\t0\t0\t0\t1.9133226526803e-34\n+mz_399.25\t0\t0\t0\t0\t0\t0\t0\t0\t8.02866831606135e-35\n+mz_399.33\t0\t0\t2.07495213544462e-05\t5.57731582375709e-05\t0\t0\t0\t0\t1.06668980736874e-35\n+mz_399.42\t0\t0\t6.47714978185832e-06\t1.83319480129285e-05\t0\t0\t0\t0\t0\n+mz_399.5\t0\t0\t5.85329928526335e-07\t1.80955305495445e-06\t0\t0\t0\t0\t0\n+mz_399.58\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.67\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.83\t0\t0\t1.3805676601919e-09\t3.41674022408256e-09\t0\t0\t0\t0\t0\n+mz_399.92\t0\t0\t8.89724960373428e-10\t2.46927300828759e-09\t0\t0\t0\t0\t0\n'

diff -r 000000000000 -r 5f18275c250a test-data/int_matrix3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix3.tabular Mon Oct 01 01:07:13 2018 -0400

diff -r 000000000000 -r 5f18275c250a test-data/kmeans_analyze.pdf

Binary file test-data/kmeans_analyze.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/loadings_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loadings_pca.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,1200 @@\n+mz\tPC1\tPC2\n+300.08\t-0.00431122859758329\t0.00526403166713949\n+300.17\t-0.000423445750267208\t0.00051702937765159\n+300.25\t4.65194150536899e-11\t-4.22150087099464e-11\n+300.33\t1.35108612188122e-11\t-1.22607072500498e-11\n+300.42\t1.05327734584566e-12\t-9.55817595104931e-13\n+300.5\t-8.10333136001904e-07\t9.89420809472527e-07\n+300.58\t-5.81387112967612e-07\t7.09876570972713e-07\n+300.67\t-1.07032789780076e-07\t1.3068757132126e-07\n+300.75\t3.41674858316537e-15\t-3.099477097213e-15\n+300.83\t1.91005306978273e-15\t-1.73400711936836e-15\n+300.92\t3.0935599995382e-16\t-2.77380998949046e-16\n+301\t-6.65648097524728e-19\t1.46948889144108e-18\n+301.08\t-6.24592367703673e-11\t7.62630392533733e-11\n+301.17\t-1.86468400473725e-11\t2.27678809866643e-11\n+301.25\t-1.54395235623673e-12\t1.88517524320557e-12\n+301.33\t2.98688326385702e-19\t-3.5847546239491e-19\n+301.42\t8.89316552145388e-20\t-1.13353541808862e-19\n+301.5\t-1.80421834428211e-18\t3.57218991846548e-18\n+301.58\t-4.42908079426941e-15\t5.40912624674897e-15\n+301.67\t-2.60749760943137e-15\t3.18475128356288e-15\n+301.75\t-4.40359280065527e-16\t5.39122160392572e-16\n+301.83\t-1.38008713975051e-18\t2.88001159253086e-18\n+301.92\t-1.40307577498072e-19\t2.77975673360276e-19\n+302\t3.62667249262872e-18\t-7.13083020490704e-18\n+302.08\t-1.08392092461489e-18\t2.3266850449903e-18\n+302.17\t-1.89685413709983e-19\t1.23861281753609e-19\n+302.25\t1.84071706842555e-19\t-4.72845441155538e-19\n+302.33\t2.65842917715123e-18\t-5.67839989734713e-18\n+302.42\t8.89384394284211e-19\t-1.78363962868074e-18\n+302.5\t-7.90254051855962e-19\t1.67197231393762e-18\n+302.58\t-2.54806306921044e-18\t4.84666648270261e-18\n+302.67\t0.00238735543431953\t0.00059717760153527\n+302.75\t0.0422753281275894\t0.0105748304975569\n+302.83\t0.0478251463644703\t0.0119630725230272\n+302.92\t0.0117873138328592\t0.00294850096557018\n+303\t0.000543891887813245\t0.000136050145022238\n+303.08\t7.47436204207542e-19\t-1.56423855319991e-18\n+303.17\t1.14392477830951e-19\t-2.37594932440985e-19\n+303.25\t-2.00896832566757e-18\t3.98635625264106e-18\n+303.33\t4.18546560129704e-06\t1.04696027795764e-06\n+303.42\t1.7855922607419e-06\t4.46651423688008e-07\n+303.5\t2.40845866549495e-07\t6.02456403664431e-08\n+303.58\t-1.26795648107974e-18\t2.62533136732221e-18\n+303.67\t-1.06780307773474e-18\t2.0810699955122e-18\n+303.75\t1.2643870416402e-18\t-2.51396059682868e-18\n+303.83\t0.00179950042171087\t-0.057307260525996\n+303.92\t0.00323910627580984\t-0.117042680086361\n+304\t-0.00221983247055412\t-0.135440075021637\n+304.08\t0.00167857919888097\t-0.0398049258709\n+304.17\t0.015254290192657\t0.012790595615181\n+304.25\t0.00615007956388472\t0.00664260824343149\n+304.33\t0.000463810193289094\t0.000732422023079692\n+304.42\t-0.0121864568041163\t-0.000404596261869822\n+304.5\t-0.0206720168643015\t-0.000503758798744126\n+304.58\t-0.0328176999234842\t-0.0126423547079233\n+304.67\t-0.0482606832428354\t-0.0105800636691633\n+304.75\t-0.0142742734952315\t-0.00471930409453522\n+304.83\t-0.00118635057916411\t-0.000662474245569403\n+304.92\t-0.00138871717853178\t-4.61060822079781e-05\n+305\t-0.0527117640926545\t-0.00175005607056224\n+305.08\t-0.0428954493028061\t-0.00142414962759593\n+305.17\t-0.00848209306364131\t-0.000281745808963649\n+305.25\t-1.99382379701303e-06\t-5.72938648410526e-07\n+305.33\t-3.36192825452903e-07\t-1.33981156083197e-07\n+305.42\t2.5761506940952e-12\t2.78245755255616e-12\n+305.5\t-3.48349631092745e-19\t7.59816858773693e-19\n+305.58\t-4.42256844036834e-06\t-1.4683141192802e-07\n+305.67\t-0.00571542047365585\t0.00879722931697928\n+305.75\t-0.0254911789946344\t0.0392460448983895\n+305.83\t-0.0105718033678137\t-0.00291019853705438\n+305.92\t0.00618064757489481\t-0.131084648437099\n+306\t-0.000838690930111978\t-0.0744131926836283\n+306.08\t-0.0130494766825355\t0.00166045771715343\n+306.17\t0.0331859098477607\t0.0161552601031249\n+306.25\t0.0699660376819185\t0.0184786284566642\n+306.33\t0.0225906387134967\t0.00565340171628555\n+306.42\t0.00212956077044587\t0.000533291798037169\n+306.5\t0.00298787533493201\t0.000738712875826988\n+306.58\t0.0950317607456352\t0.0237696453640889\n+306.67\t0.12310606507388\t0.0260031521356849\n+306.75\t0.0306645997652937\t-0.0571'..b'23546721038e-12\n+393.25\t-2.34036390405774e-11\t4.93900212123262e-13\n+393.33\t-3.56838704124608e-06\t4.07205506770384e-06\n+393.42\t-1.76198360856187e-06\t2.01068275372772e-06\n+393.5\t-0.00233992195400915\t0.00360244123900651\n+393.58\t-0.0224309026287285\t0.0345346530641351\n+393.67\t-0.0144781756530043\t0.0222906220696274\n+393.75\t-0.0026549293256643\t0.00408753337701366\n+393.83\t-3.04582339785289e-11\t3.47569898364536e-11\n+393.92\t-2.07692010278724e-10\t2.37007166468918e-10\n+394\t0.000989421728722559\t-0.0315093316645265\n+394.08\t0.00166917857982581\t-0.0531570081597263\n+394.17\t0.000515223006487019\t-0.0164551396233416\n+394.25\t4.55292483933701e-05\t-0.00146398008581852\n+394.33\t-3.80471565270782e-08\t5.85774621944284e-08\n+394.42\t-1.80262500024233e-14\t2.05689490369655e-14\n+394.5\t-7.7909656610118e-15\t8.88828831877814e-15\n+394.58\t1.12421356224445e-07\t-3.58019391594558e-06\n+394.67\t7.11020518802956e-08\t-2.26769779930263e-06\n+394.75\t0.000316047453349314\t-0.0100649148736834\n+394.83\t0.00229889763821647\t-0.073211172468377\n+394.92\t0.00150372971795886\t-0.0478880892309078\n+395\t0.000292705972843111\t-0.00932157526617029\n+395.08\t-0.00875103820451387\t0.00998622320294566\n+395.17\t-0.0126456283855077\t0.0144305240873075\n+395.25\t-0.00378465244012699\t0.00431884573343672\n+395.33\t-0.000315001652628076\t0.000359463270406603\n+395.42\t1.56478579106423e-07\t-4.9832493669199e-06\n+395.5\t4.95699913407887e-08\t-1.57861625005459e-06\n+395.58\t4.59965931477345e-09\t-1.46481706778349e-07\n+395.67\t-8.93363646461732e-07\t1.01945947057533e-06\n+395.75\t-5.28499859979223e-07\t6.03096163123705e-07\n+395.83\t0.0101721470821755\t0.00254460417531899\n+395.92\t0.0901124169298955\t0.0225408899978156\n+396\t0.0619057408174025\t0.0154852188209358\n+396.08\t0.0120686207083509\t0.00301886756043136\n+396.17\t2.13427762585755e-18\t-4.57591641293874e-18\n+396.25\t-5.93693477596822e-11\t6.77491676579856e-11\n+396.33\t-1.62663136152525e-11\t1.85622572248383e-11\n+396.42\t-1.09391652965735e-12\t1.24832003417318e-12\n+396.5\t6.43609376126285e-06\t1.60993663686421e-06\n+396.58\t2.04220500508587e-06\t5.10841013808235e-07\n+396.67\t1.90042568568878e-07\t4.75376068364845e-08\n+396.75\t-4.67251518868319e-15\t5.33097853187915e-15\n+396.83\t-2.35613979840554e-15\t2.69012387669633e-15\n+396.92\t-3.61561868840093e-16\t4.1275441396577e-16\n+397\t0.00683320944088087\t0.00170927192743568\n+397.08\t0.0508156173515183\t0.0127111145890864\n+397.17\t0.0315399671799999\t0.00788946701538054\n+397.25\t0.00571098525966419\t0.00142855664922875\n+397.33\t4.89969485396192e-19\t-1.19060334525639e-18\n+397.42\t2.22834919338454e-18\t-4.34732897976762e-18\n+397.5\t8.31147483196322e-19\t-1.78218120586324e-18\n+397.58\t7.14897520004991e-19\t-1.54051878724343e-18\n+397.67\t3.41887735034728e-06\t8.55204443656831e-07\n+397.75\t1.0035305688935e-06\t2.51025033637385e-07\n+397.83\t8.01158365214818e-08\t2.00403268096558e-08\n+397.92\t-1.9142113485302e-18\t3.69209812345875e-18\n+398\t-2.33556706483865e-18\t4.5182654397614e-18\n+398.08\t-0.00206607196679601\t0.00235769234822122\n+398.17\t-0.0225874349565933\t0.0257755896848458\n+398.25\t-0.0160218359330536\t0.0182832742502864\n+398.33\t-0.0026940895995632\t0.00307435297682499\n+398.42\t-3.76104775049341e-18\t8.41246115765971e-18\n+398.5\t2.39548120740311e-20\t-5.08280982949083e-20\n+398.58\t5.66389784439603e-19\t-1.12520168973942e-18\n+398.67\t0.00295354336564466\t0.0016465989339032\n+398.75\t0.100753555082997\t0.0424027103707126\n+398.83\t0.0858729519853825\t0.0359862357359944\n+398.92\t0.0173733382364934\t0.00713147150476632\n+399\t4.58678491672166e-19\t-1.05711764259232e-18\n+399.08\t-3.74124159573477e-18\t8.10123796770424e-18\n+399.17\t1.44107919235719e-18\t-2.94492407411307e-18\n+399.25\t-2.28306806332197e-18\t4.56015944945022e-18\n+399.33\t8.7259811334237e-06\t3.70432674670869e-06\n+399.42\t2.88619885891337e-06\t1.19693828706317e-06\n+399.5\t2.87745593745991e-07\t1.14900342939911e-07\n+399.58\t3.43909756603207e-18\t-7.1235425369153e-18\n+399.67\t5.41775952563231e-19\t-1.17632377804067e-18\n+399.75\t-2.94880449307325e-20\t5.68563417987762e-20\n+399.83\t5.28798133253926e-10\t2.33513647021011e-10\n+399.92\t3.87854520523766e-10\t1.62263513454245e-10\n'

diff -r 000000000000 -r 5f18275c250a test-data/mean_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_out2.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,3673 @@\n+mz_name\tcol1\tcol2\tcol3\n+mz_1199.47\t30\t10.6666666666667\t21.6666666666667\n+mz_1199.51\t40\t13.6666666666667\t30.6666666666667\n+mz_1199.56\t49.3333333333333\t12.3333333333333\t39.3333333333333\n+mz_1199.6\t48\t14.3333333333333\t37.6666666666667\n+mz_1199.64\t39\t11\t32.3333333333333\n+mz_1199.68\t28.3333333333333\t10.6666666666667\t29.6666666666667\n+mz_1199.72\t22.3333333333333\t10\t18.6666666666667\n+mz_1199.76\t20.3333333333333\t9.33333333333333\t16.3333333333333\n+mz_1199.8\t17.3333333333333\t8.33333333333333\t15.3333333333333\n+mz_1199.85\t15.6666666666667\t7\t13\n+mz_1199.89\t13\t8.66666666666667\t12\n+mz_1199.93\t10.3333333333333\t8.66666666666667\t10\n+mz_1199.97\t11.6666666666667\t8.66666666666667\t9.33333333333333\n+mz_1200.01\t11.6666666666667\t8.33333333333333\t9.33333333333333\n+mz_1200.05\t10.6666666666667\t6.33333333333333\t7.66666666666667\n+mz_1200.09\t13\t9.33333333333333\t9.66666666666667\n+mz_1200.14\t11.6666666666667\t8\t9.33333333333333\n+mz_1200.18\t9.33333333333333\t9\t8.66666666666667\n+mz_1200.22\t10.3333333333333\t7.66666666666667\t9.33333333333333\n+mz_1200.26\t10.6666666666667\t6.66666666666667\t9.66666666666667\n+mz_1200.3\t10.3333333333333\t6.66666666666667\t10\n+mz_1200.34\t13.3333333333333\t9.66666666666667\t14.3333333333333\n+mz_1200.38\t16.3333333333333\t9.33333333333333\t12\n+mz_1200.42\t15.3333333333333\t9\t14.3333333333333\n+mz_1200.47\t19\t9\t15.6666666666667\n+mz_1200.51\t24.3333333333333\t11.3333333333333\t22.3333333333333\n+mz_1200.55\t29\t10.6666666666667\t21.6666666666667\n+mz_1200.59\t28.3333333333333\t11\t22.3333333333333\n+mz_1200.63\t25\t9.33333333333333\t18\n+mz_1200.67\t19.6666666666667\t8.66666666666667\t17.3333333333333\n+mz_1200.71\t17.6666666666667\t7.66666666666667\t12.3333333333333\n+mz_1200.76\t14.3333333333333\t8.33333333333333\t12\n+mz_1200.8\t14\t7.33333333333333\t10.6666666666667\n+mz_1200.84\t11.3333333333333\t7.66666666666667\t11\n+mz_1200.88\t11.3333333333333\t8.33333333333333\t10.3333333333333\n+mz_1200.92\t9\t8.66666666666667\t10.3333333333333\n+mz_1200.96\t11\t7\t8.66666666666667\n+mz_1201\t10.3333333333333\t9\t9.66666666666667\n+mz_1201.05\t10\t7.66666666666667\t9.33333333333333\n+mz_1201.09\t9.33333333333333\t8.33333333333333\t9.33333333333333\n+mz_1201.13\t11\t7.66666666666667\t9\n+mz_1201.17\t10\t8.33333333333333\t9\n+mz_1201.21\t10.3333333333333\t8.66666666666667\t10.3333333333333\n+mz_1201.25\t11.3333333333333\t7.33333333333333\t9\n+mz_1201.29\t12.3333333333333\t8.33333333333333\t9\n+mz_1201.33\t13.3333333333333\t10\t12\n+mz_1201.38\t19.3333333333333\t9\t11\n+mz_1201.42\t21.6666666666667\t9.66666666666667\t16.3333333333333\n+mz_1201.46\t20.6666666666667\t11\t17.3333333333333\n+mz_1201.5\t20.3333333333333\t9.66666666666667\t16\n+mz_1201.54\t21\t9.66666666666667\t18\n+mz_1201.58\t19.6666666666667\t9.33333333333333\t18\n+mz_1201.62\t15.6666666666667\t8.33333333333333\t12\n+mz_1201.67\t15\t7.33333333333333\t11.3333333333333\n+mz_1201.71\t14\t9\t11.6666666666667\n+mz_1201.75\t11.6666666666667\t7\t11.3333333333333\n+mz_1201.79\t13.3333333333333\t8\t10\n+mz_1201.83\t10\t7\t9.66666666666667\n+mz_1201.87\t11.6666666666667\t7\t9\n+mz_1201.91\t9.33333333333333\t7.66666666666667\t8.33333333333333\n+mz_1201.96\t11\t7.66666666666667\t9.66666666666667\n+mz_1202\t9\t7\t9.33333333333333\n+mz_1202.04\t10.3333333333333\t7\t8\n+mz_1202.08\t9.66666666666667\t8\t7.66666666666667\n+mz_1202.12\t9.33333333333333\t7.33333333333333\t7.66666666666667\n+mz_1202.16\t10\t8\t10\n+mz_1202.2\t11\t8\t9.33333333333333\n+mz_1202.25\t11.3333333333333\t8.33333333333333\t10\n+mz_1202.29\t13\t7.33333333333333\t8\n+mz_1202.33\t13\t8.33333333333333\t11\n+mz_1202.37\t14.6666666666667\t9.66666666666667\t12\n+mz_1202.41\t15.3333333333333\t8.33333333333333\t11.3333333333333\n+mz_1202.45\t18.3333333333333\t10\t11\n+mz_1202.49\t15.6666666666667\t9.33333333333333\t13.6666666666667\n+mz_1202.54\t16\t8\t14.3333333333333\n+mz_1202.58\t14.3333333333333\t8\t13.6666666666667\n+mz_1202.62\t14\t8\t13\n+mz_1202.66\t11.3333333333333\t8.33333333333333\t11.6666666666667\n+mz_1202.7\t10.3333333333333\t7.33333333333333\t9.66666666666667\n+mz_1202.74\t11\t9\t9.66666666666667\n+mz_1202.78\t12.3333333333333\t7.66666666666667\t8.66666666666667\n+mz_1202.83\t10.3333333333333\t7.66666666666667\t9.66666666666667\n+mz_1202.8'..b'6667\n+mz_1352.43\t11.6666666666667\t9\t10.3333333333333\n+mz_1352.47\t13.3333333333333\t8.66666666666667\t11.3333333333333\n+mz_1352.52\t12.3333333333333\t7.66666666666667\t8.66666666666667\n+mz_1352.56\t9.66666666666667\t9\t9.66666666666667\n+mz_1352.61\t12\t7.66666666666667\t10.3333333333333\n+mz_1352.65\t11.6666666666667\t6.66666666666667\t8\n+mz_1352.69\t12.3333333333333\t8\t8.33333333333333\n+mz_1352.74\t9.33333333333333\t8\t10\n+mz_1352.78\t11\t6.66666666666667\t9.33333333333333\n+mz_1352.83\t10\t8.33333333333333\t9\n+mz_1352.87\t9.33333333333333\t7\t9.66666666666667\n+mz_1352.91\t9.66666666666667\t7.66666666666667\t9.33333333333333\n+mz_1352.96\t9.66666666666667\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 5f18275c250a test-data/msidata_1.RData

Binary file test-data/msidata_1.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/msidata_2.RData

Binary file test-data/msidata_2.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/msidata_3.RData

Binary file test-data/msidata_3.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/pca_imzml.pdf

Binary file test-data/pca_imzml.pdf has changed

diff -r 000000000000 -r 5f18275c250a 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 01:07:13 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 5f18275c250a test-data/pixel_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out2.tabular Mon Oct 01 01:07:13 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 5f18275c250a test-data/pixel_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out3.tabular Mon Oct 01 01:07:13 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 5f18275c250a test-data/pixels_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test2.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,25 @@
+pixel names x y predicted condition
+xy_1_1 1 1 A
+xy_2_1 2 1 A
+xy_3_1 3 1 A
+xy_4_1 4 1 A
+xy_1_2 1 2 B
+xy_2_2 2 2 B
+xy_3_2 3 2 B
+xy_4_2 4 2 B
+xy_1_3 1 3 C
+xy_2_3 2 3 C
+xy_3_3 3 3 C
+xy_4_3 4 3 C
+xy_10_1 10 1 A
+xy_11_1 11 1 A
+xy_12_1 12 1 A
+xy_13_1 13 1 A
+xy_10_2 10 2 B
+xy_11_2 11 2 B
+xy_12_2 12 2 B
+xy_13_2 13 2 B
+xy_10_3 10 3 B
+xy_11_3 11 3 C
+xy_12_3 12 3 C
+xy_13_3 13 3 C

diff -r 000000000000 -r 5f18275c250a test-data/pixels_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test4.tabular Mon Oct 01 01:07:13 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 5f18275c250a test-data/pixels_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test6.tabular Mon Oct 01 01:07:13 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
+xy_11_2 11 2 B
+xy_12_2 12 2 A
+xy_13_2 13 2 B
+xy_10_3 10 3 A
+xy_11_3 11 3 A
+xy_12_3 12 3 B
+xy_13_3 13 3 A

diff -r 000000000000 -r 5f18275c250a test-data/pixels_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test7.tabular Mon Oct 01 01:07:13 2018 -0400

diff -r 000000000000 -r 5f18275c250a test-data/preprocessed.RData

Binary file test-data/preprocessed.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessed.rdata

Binary file test-data/preprocessed.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results1.RData

Binary file test-data/preprocessing_results1.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results1.pdf

Binary file test-data/preprocessing_results1.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.txt Mon Oct 01 01:07:13 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 5f18275c250a test-data/preprocessing_results2.RData

Binary file test-data/preprocessing_results2.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results2.pdf

Binary file test-data/preprocessing_results2.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.txt Mon Oct 01 01:07:13 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 = 3\n+200.833343505859\t0\t0\t0\t0\t29.7300018610011\t0\t20.3366320492341\t0\t0\n+201.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+202\t0\t0\t0\t0\t0\t0\t0\t0\t23.1435050872708\n+202.833343505859\t0\t0\t0\t0\t0\t0\t0\t32.8864858064308\t8.10338356295316\n+203.833343505859\t51.2049601068229\t0\t11.3700059373061\t0\t0\t0\t0\t0\t0\n+204.16667175293\t0\t0\t0\t15.6578509107164\t17.287114514836\t0\t29.3801156200759\t0\t0\n+205.083343505859\t28.0632538418884\t0\t0\t14.0803616432178\t0\t0\t0\t0\t0\n+205.66667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+206.16667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+206.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+207.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+207.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+208.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+208.91667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+210.333343505859\t0\t0\t16.0744032361685\t0\t0\t0\t0\t0\t0\n+210.91667175293\t0\t15.9820002415152\t0\t0\t0\t0\t0\t0\t0\n+211.41667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+212\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+212.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+213.16667175293\t0\t15.2652007909183\t0\t10.8255187125352\t0\t0\t0\t19.8092361623607\t26.1478463765446\n+213.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+214.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+214.833343505859\t0\t0\t20.2607669942264\t0\t0\t0\t0\t0\t22.2161013291355\n+215.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+216.16667175293\t0\t18.3609620294097\t0\t0\t0\t0\t0\t0\t0\n+217\t37.5783693521794\t0\t0\t0\t0\t0\t0\t0\t17.69680049\n+217.91667175293\t0\t0\t0\t0\t0\t0\t0\t21.5182960927257\t0\n+218.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+219\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+219.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+220.16667175293\t0\t18.6457852489373\t32.9506894838222\t24.0912426231137\t31.7570178011101\t0\t0\t26.1970193149565\t0\n+220.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+221.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+222.16667175293\t0\t0\t0\t0\t14.9277079269749\t0\t0\t0\t9.24959754459775\n+222.833343505859\t0\t0\t0\t0\t0\t0\t0\t26.6440210634237\t0\n+223.083343505859\t0\t0\t0\t0\t0\t0\t23.5238209819287\t0\t0\n+224.083343505859\t0\t0\t0\t0\t32.4650140432206\t0\t0\t0\t0\n+225\t20.8388438079399\t0\t0\t0\t0\t0\t0\t0\t0\n+225.75\t0\t0\t0\t0\t0\t32.071221564219\t0\t0\t0\n+226.333343505859\t30.367702170641\t0\t0\t15.9340302645031\t0\t0\t0\t0\t15.166781328744\n+227.25\t61.00694174083\t18.2774565189601\t33.1378572944533\t14.1126101567404\t60.3708882185737\t69.1182306806\t88.3890204657392\t17.9301928152478\t18.5442887505179\n+228.25\t0\t0\t0\t19.7973152451708\t29.1284464743225\t0\t48.1255937132277\t0\t11.2418187281387\n+228.833343505859\t0\t0\t0\t0\t39.2881990234499\t0\t0\t23.571813759223\t9.49534330127652\n+230.16667175293\t0\t0\t0\t0\t0\t0\t0\t13.7350515954528\t0\n+230.66667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+232\t0\t31.5564252752125\t39.7840997448739\t19.5226243226405\t0\t0\t17.545727945806\t16.2769262883882\t0\n+233.25\t0\t0\t23.2862438784232\t0\t0\t0\t28.5339722091309\t29.9587504979069\t0\n+233.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+234.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+235.25\t0\t0\t0\t0\t0\t0\t0\t0\t13.9555220480511\n+236\t0\t22.7227304002729\t0\t0\t0\t0\t0\t0\t0\n+236.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+237.083343505859\t0\t18.0553170060993\t0\t0\t0\t0\t0\t0\t0\n+237.91667175293\t0\t0\t0\t0\t0\t0\t0\t17.1121940150021\t0\n+238.41667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+239\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+239.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+240.083343505859\t0\t0\t0\t0\t28.5240458569983\t0\t0\t25.0985019862697\t0\n+241.333343505859\t32.9293862937878\t18.5131385791316\t0\t33.5594440580247\t29.597702335892\t0\t52.7104324295036\t24.0717290213301\t31.8650142730283\n+242.083343505859\t0\t17.787078739077\t0\t0\t13.9279312472109\t43.8891095673046\t30.2546875982475\t36.1208669086842\t0\n+243.083343505859\t0\t0\t0\t0\t0\t0\t15.5592808318967\t0\t12.3958830399374\n+243.66667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+244.16667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+244.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t12.8490140044155\n+245.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+246.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+246.66667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+247.66667175293\t0\t0\t0\t0\t21.7950679804068\t0\t0\t22.4977174800829\t0\n+248.16667175293\t0\t0\t0\t0\t0\t33.5978649704311\t0\t25.893190934143\t0\n+248.5\t0\t0\t0\t18.158696915579\t0\t0\t0\t0\t0\n+249.25\t18.7903925680504\t0\t0\t0\t0\t0\t0\t0\t0\n+249.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+250.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+251.16667175293\t0\t0\t0\t0\t32.4071326541188\t0\t0\t0\t11.9615597726954\n+251.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+252.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+253.16667175293\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+253.666671752'..b'\t0\t0\t0\t0\t0\t0\t0\n+338.166687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+338.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+339.416687011719\t0\t0\t0\t0\t39.8603419770766\t0\t0\t0\t0\n+339.916687011719\t0\t0\t0\t0\t20.858069520381\t0\t0\t0\t0\n+340.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+341\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+341.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+342.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t19.6664686760846\n+343\t0\t24.9136218471955\t0\t32.344625078576\t0\t0\t30.0229321228603\t0\t0\n+344\t0\t38.4142619483613\t0\t51.4185116656209\t15.7674653573169\t0\t0\t31.3565353900891\t29.5640946328953\n+345\t89.440808882377\t64.3979976515781\t69.0676509315537\t28.9295335285171\t28.9161160500209\t82.4933661280555\t43.6333514610303\t42.8223438499387\t23.3642044056771\n+345.5\t0\t17.9053906829632\t0\t0\t26.7716187236005\t0\t0\t22.3332379850821\t58.1091304877784\n+346\t0\t56.3824132218771\t0\t39.0036223920686\t0\t22.0938155709768\t0\t0\t24.1426944514917\n+346.916687011719\t0\t20.8340351852125\t0\t22.6652681842216\t14.8696905661875\t0\t0\t15.618325524579\t0\n+350.083343505859\t0\t14.2632499913526\t0\t0\t0\t0\t0\t0\t0\n+350.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+351.166687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+351.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+352.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+353.083343505859\t0\t0\t0\t0\t0\t0\t16.8234524228888\t0\t0\n+353.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+354.166687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+355.333343505859\t0\t0\t0\t0\t0\t0\t18.490727196134\t0\t22.5833915337106\n+355.916687011719\t0\t0\t0\t15.6092670198485\t0\t0\t0\t0\t0\n+356.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+356.916687011719\t0\t0\t0\t0\t0\t0\t25.8992783836766\t0\t0\n+357.333343505859\t0\t0\t0\t0\t0\t0\t0\t19.7877173158758\t0\n+357.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+358.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+358.916687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+359.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+359.916687011719\t0\t0\t15.2291980667164\t0\t14.8664189209361\t0\t0\t0\t0\n+360.916687011719\t32.9744131371326\t0\t0\t0\t0\t0\t0\t0\t0\n+361.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+362\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+362.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+363.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+363.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+364.333343505859\t57.7406498654606\t0\t0\t0\t0\t0\t0\t0\t0\n+364.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+365.833343505859\t0\t0\t0\t23.7421226644684\t46.0960367777783\t0\t19.4362629084055\t0\t0\n+366.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+367.916687011719\t0\t31.1089967560267\t0\t0\t0\t0\t0\t0\t0\n+368.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+369.083343505859\t0\t23.2062449204231\t0\t0\t0\t0\t0\t0\t0\n+370.333343505859\t30.8381452757664\t0\t49.5953209142812\t0\t0\t0\t0\t19.4647918141462\t0\n+370.916687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+371.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+372\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+372.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+373.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+373.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+374.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+375.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+376\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+376.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t12.4108436848343\n+377.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+377.916687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+378.75\t0\t12.4414396381466\t0\t0\t0\t0\t0\t0\t0\n+379.5\t0\t0\t21.5287688898373\t0\t0\t0\t0\t0\t0\n+380.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+380.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+381.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+381.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+382.583343505859\t0\t0\t0\t0\t20.7893695949884\t0\t0\t0\t0\n+383.166687011719\t0\t0\t0\t0\t36.2220726623636\t0\t0\t0\t0\n+383.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+384.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+384.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+385.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+385.833343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+386.75\t0\t0\t0\t0\t0\t0\t0\t14.7399918416133\t0\n+387.166687011719\t0\t0\t0\t0\t0\t0\t0\t0\t22.0763041955615\n+387.5\t0\t0\t21.1178263931554\t0\t0\t15.3290299771848\t0\t0\t0\n+388.25\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+389.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+390.166687011719\t0\t0\t0\t0\t0\t21.9188439739601\t0\t0\t0\n+391.083343505859\t0\t0\t0\t0\t0\t24.0561456663434\t0\t0\t0\n+392\t0\t0\t0\t0\t0\t42.9985558418334\t0\t0\t0\n+392.833343505859\t0\t0\t41.1465765853643\t0\t0\t0\t0\t0\t0\n+393.583343505859\t0\t0\t0\t0\t0\t0\t0\t20.4528870846676\t0\n+394.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+395.166687011719\t0\t0\t12.4535077266748\t0\t0\t0\t0\t0\t10.7085862343913\n+395.916687011719\t0\t0\t0\t21.3907076844532\t0\t0\t0\t0\t0\n+396.5\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+397.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+397.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+398.166687011719\t0\t0\t22.2442721127594\t0\t0\t0\t0\t0\t0\n+398.75\t0\t0\t12.1748320091567\t26.8513023565384\t0\t0\t0\t0\t0\n+399.333343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n'

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results3.RData

Binary file test-data/preprocessing_results3.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results3.pdf

Binary file test-data/preprocessing_results3.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results4.RData

Binary file test-data/preprocessing_results4.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results4.pdf

Binary file test-data/preprocessing_results4.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.txt Mon Oct 01 01:07:13 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 5f18275c250a test-data/preprocessing_results5.RData

Binary file test-data/preprocessing_results5.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results5.pdf

Binary file test-data/preprocessing_results5.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/preprocessing_results5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.txt Mon Oct 01 01:07:13 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
+301 0 0 0 0 0 0 0 0 0
+302 0 4.32197925754431e-23 0 0 0 0 0 0 0
+303 0 1.28620729883923e-30 0 0.00308917369693518 0 0 0 0 0
+304 0 1.32924944261294e-38 0 2.8316210487489e-10 0.411686420440674 0 0 0 0.609295308589935
+305 0 0 0 5.69736818276873e-18 0 0 0.716848015785217 0 0
+306 0 0.180751591920853 0.0924000516533852 3.22355374818131e-26 0.228940084576607 0 0 0 0.338278532028198
+307 5.31794802036641e-23 1.36712752230039e-09 0 0.503042221069336 0.171210870146751 0 0 0.0994685217738152 0.00513129541650414
+308 1.42257959582276e-30 0 0 0 0 0 0 0.0315862037241459 0.322940319776535
+309 1.43981749664202e-38 2.37613022591177e-07 0 0 1.4921518187716e-10 0 7.17280070103395e-32 1.14764100445086e-08 0
+310 0 2.2688041766486e-14 0.0299898684024811 0 4.55189177922775e-18 0 0 2.89623705606364e-14 0
+311 0 4.60080996999485e-22 9.34697319543432e-10 3.53486932303922e-32 5.44664266518465e-26 0 0 6.9618325415624e-22 0
+312 0 0 1.14256191537071e-17 0 0 0 0 6.04272858040201e-30 1.25046502952903e-32
+313 0 0 0 0 0 0 0 0.000948468048591167 0
+314 0 0.343302994966507 0 0 0 0 0 0 0
+315 0 0 0.12950636446476 0 0 0 0 0 0
+316 0.327463179826736 0 1.93941795956221e-09 0.00699668889865279 0 0 0 0.0240590367466211 0
+317 1.18278642435854e-09 0 0 1.591814253743e-07 0 0 0 7.10978553808417e-10 0
+318 0 2.88274619950529e-32 0.312686443328857 1.89643697338752e-14 0 0 0 8.22819137337219e-18 0
+319 0 0 3.68662113032769e-05 3.99332497384422e-22 0 0 0 0 0
+320 0 0 5.68011697044319e-15 2.58921175367487e-30 0 0 0 0 0
+321 0 0 0 0 0 0 0.0821415111422539 0 0
+322 0 0 0 0 0 0 1.23654897432601e-09 8.91581066753133e-07 0
+323 0 0 0 0 0 0 0 3.62019611608189e-14 0
+324 0 0 0 0 0 0 1.41676795295531e-10 5.43261166662179e-22 0
+325 0 0 0 0 0 0 3.87320208074687e-18 0 0
+326 0 0 0 0 0 0 4.08673089735238e-26 0 0.0913732051849365
+327 0.0852032229304314 0 0 0.539452373981476 0 0 0.313083916902542 0 0.335682272911072
+328 0.12766021490097 0 0.454382658004761 0.058334868401289 0 0 2.71850386646122e-09 0.849055886268616 0.565727531909943
+329 2.21637320518494 1.62591469287872 0.87499076128006 2.59215974807739 0.914434671401978 0.544950544834137 0.609484612941742 1.3272477388382 1.07743680477142
+330 0 0.282970458269119 0 0.414683222770691 0 0.386884957551956 0 0.0383349843323231 0
+331 0 0 0 0 1.48969615668734e-14 0 1.53340424261178e-14 0 0
+332 9.75976108698449e-24 0 1.9129100416656e-25 0 3.87271811263777e-22 0 4.34332980949855e-22 4.19115925707927e-15 2.22326423345091e-22
+333 2.46229240610247e-30 0.292759567499161 8.11414880231369e-31 0 3.81384647033894e-30 0 4.78893314027823e-30 3.07998888597304e-22 5.63234713964859e-30
+334 5.59128344770361e-38 2.16568318833765e-09 1.95524197675121e-38 3.50986532392816e-31 0 0.0106925405561924 0 5.88708673366388e-30 5.33374608969737e-38
+335 0 0 0 0 0 0 0.188220098614693 2.75847732676006e-38 0
+336 0 0 7.14956786396215e-06 0 0 0 2.40733255552072e-09 0 0
+337 0 0 9.22569177086094e-14 0 0 1.92654253432319e-23 0.129606500267982 0 0
+338 0 0 0 0 0 8.21688042580719e-31 0 0 0
+339 0 0 0 0 0 1.2691101966792e-38 0 0 0
+340 0 0 0 0 0.131738051772118 0 0 0 0
+341 0 0 0 0 1.97074911945094e-09 0 2.68033400688056e-31 0 0
+342 0 0 0 0 0 0 0 0 0
+343 0 0.540803730487823 0 0.311067968606949 0 0 0.456998586654663 0 1.1592504051805e-05
+344 0 0.760098695755005 0 1.23029351234436 0.179359897971153 0 0 0 0.385462760925293
+345 1.29758274555206 1.30673027038574 0.626297771930695 0.370624721050262 0.266427725553513 0.95829576253891 0.664171636104584 0.340830773115158 0.920338690280914
+346 0 1.22390151023865 0 0.25139981508255 0 0.280698895454407 0 0 0.700047612190247
+347 0 0.0356887876987457 0 0.208728492259979 0 0 0 0.0668430551886559 0
+348 0 9.81050796156069e-10 5.19627293105376e-24 2.63146238133061e-09 0 0 9.31592096266419e-23 1.41976275180866e-09 0
+349 0 1.04223425420895e-17 6.50702138942878e-31 0 3.61575250654619e-19 0 2.28809034992078e-30 9.42402156952173e-18 0
+350 0 0.0264999140053988 1.43329403190105e-38 0 1.18586093356332e-26 7.10052307988494e-32 2.00786591889092e-38 0 4.14061161573622e-23
+351 0 0 0 0 1.5203838193817e-34 0 0 0 1.16283201971478e-30
+352 0 0 0 0 0 0 0 0 1.26231628133462e-38
+353 0 1.38150654422023e-23 0 0 0 0 0.205960765480995 0 0
+354 0 7.25574687381216e-31 0 0 0 0 0 0 0
+355 0 1.23978031917165e-38 0 0 0 0 0.00283639249391854 0 0
+356 0 0 0 0.121438764035702 0 0 0 0 1.23199033623678e-05
+357 0 0 0 1.77123560263226e-09 0 0 0.182004451751709 0 1.95739488528281e-13
+358 0 0 0 0 0 0 1.98827221353781e-09 1.78993400368199e-06 1.41009214974392e-22
+359 0 0 0 0 0 0 0 6.27455241084852e-14 0
+360 0 0 0.108914941549301 0 0.137880623340607 0 0 8.50402759093013e-22 0
+361 0.195893675088882 0 1.41621303573203e-09 0 1.26956511969922e-09 0 0 0 0
+362 2.35806374426772e-09 0 0 0 0 0 0 0 0
+363 0 0 0 0 0 0 0 0 0
+364 0 0 0 0 0 0 0 0 0
+365 4.718969194073e-06 0 0 0 0 0 0 0 0
+366 1.5078418385845e-13 0 0 0 0.0833132043480873 0 0.00646991981193423 0 0
+367 1.88767583715038e-21 0 0 0 1.99935068501134e-09 0 0 0 0
+368 0 0.240184053778648 0 0 1.73021765774411e-17 0 0 0 0
+369 0 0 0 2.14222150679164e-28 0 0 1.8149379644405e-23 0 0
+370 0.220073893666267 0 0 5.0712002936768e-35 0 0 8.36182452163646e-31 0 0
+371 0 0 1.01167734101182e-05 0 0 0 1.34585889318073e-38 1.26896829897305e-05 0
+372 0 2.36356311389003e-23 2.1724240245255e-13 0 0 0 0 1.94110095293361e-13 0
+373 0 1.28305368259484e-30 1.48263228973474e-21 0 0 0 0 0 0
+374 2.51170957735397e-31 2.22206616007007e-38 0 0 0 0 0 0 0
+375 0 0 0 4.09362382924883e-06 0 0 0 0 0
+376 0 0.25187474489212 0 0 0 0 0 0 0
+377 0 0 0 0 0 0 0 0 0.0245788525789976
+378 0 0 0 0 0 0 0 0 7.31565030775982e-10
+379 0 0 0 4.74098883507114e-36 0 0 0 0 8.53033646290005e-18
+380 0 5.35888382280358e-11 0 0 0 0 0 0 0
+381 0 2.08035531146295e-18 0 0 0 0 0 0 0
+382 0 3.03360559481662e-26 1.34763172843222e-11 0 0 0 0 0 0
+383 0 0 9.92826425348915e-19 0 0 0 0 0 0
+384 0 0 1.89875384027677e-26 0 0 0 0 0 0
+385 0 0 8.90882200712694e-35 0 0 0 0 0 0
+386 0 0 0 0 5.48654842174003e-23 0 0 0 0
+387 0 0 0 0 1.95871382355483e-30 0 0 0 0.445850938558578
+388 0 0 2.8698808819172e-05 0 2.6922900766543e-38 0 0 2.03287057326529e-11 0
+389 0 0 0 0 0 0 0 1.5199915248611e-18 1.14508647721767e-14
+390 0 0 0 0 0 5.99971986065457e-19 0 2.91871447509579e-26 3.90949821591828e-22
+391 0 0 0 0 0 0.0269051976501942 0 1.39327729380305e-34 5.18557991695755e-30
+392 0 0 9.13119889883398e-37 0 0 0.554931581020355 0 0 0
+393 0 0 0.0149336429312825 0 0 0 0 0 0
+394 0 0 9.79982650584077e-10 0 0 0 0 0 0.133639797568321
+395 0 0 0 0 0 0 0 0 0.0395353808999062
+396 0 0 0 0.35160955786705 0 4.33367092554234e-32 0 0 9.14517350736332e-10
+397 0 0 0 0.0388109683990479 0 0 0 3.20919536266692e-27 7.3794850397387e-18
+398 0 0 2.73956025372824e-23 0 0 0 0 1.02695755303769e-34 0
+399 0 0 0 0 0 0 0 0 0

diff -r 000000000000 -r 5f18275c250a test-data/random_factors.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_factors.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,24 @@
+1 1 f1 A
+2 1 f1 A
+3 1 f2 B
+4 1 f1 C
+1 2 f2 C
+2 2 f2 C
+3 2 f2 B
+4 2 f2 A
+1 3 f2 A
+2 3 f1 B
+3 3 f2 C
+4 3 f1 A
+10 1 f1 A
+11 1 f2 C
+12 1 f1 B
+13 1 f1 B
+10 2 f1 B
+11 2 f1 A
+12 2 f2 C
+13 2 f2 A
+10 3 f1 C
+11 3 f2 B
+12 3 f1 B
+13 3 f2 C

diff -r 000000000000 -r 5f18275c250a test-data/rdata_notfiltered.RData

Binary file test-data/rdata_notfiltered.RData has changed

diff -r 000000000000 -r 5f18275c250a test-data/rdata_notfiltered.pdf

Binary file test-data/rdata_notfiltered.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/scores_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scores_pca.tabular Mon Oct 01 01:07:13 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
+xy_2_3 2 3 -1.08833133183905 1.16461090511219
+xy_3_3 3 3 0.147195401291175 -3.25809198000829

diff -r 000000000000 -r 5f18275c250a test-data/sd_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sd_out2.tabular Mon Oct 01 01:07:13 2018 -0400

b'@@ -0,0 +1,3673 @@\n+mz name\tcol1\tcol2\tcol3\n+mz_1199.47\t9.8488578017961\t1.52752523165195\t1.15470053837925\n+mz_1199.51\t14.7309198626562\t4.72581562625261\t2.08166599946613\n+mz_1199.56\t27.4286954362276\t3.05505046330389\t7.50555349946513\n+mz_1199.6\t31.1929479209644\t8.50490054811538\t5.68624070307733\n+mz_1199.64\t20.0748598998847\t3.60555127546399\t1.52752523165195\n+mz_1199.68\t12.0968315410827\t3.05505046330389\t5.85946527708232\n+mz_1199.72\t8.38649708360608\t3.60555127546399\t3.21455025366432\n+mz_1199.76\t7.76745346515403\t2.3094010767585\t2.88675134594813\n+mz_1199.8\t7.76745346515403\t0.577350269189626\t3.21455025366432\n+mz_1199.85\t4.72581562625261\t1\t0\n+mz_1199.89\t3.60555127546399\t2.08166599946613\t2\n+mz_1199.93\t1.15470053837925\t2.3094010767585\t1.73205080756888\n+mz_1199.97\t1.52752523165195\t1.52752523165195\t1.15470053837925\n+mz_1200.01\t1.15470053837925\t1.52752523165195\t0.577350269189626\n+mz_1200.05\t0.577350269189626\t1.52752523165195\t1.15470053837925\n+mz_1200.09\t2.64575131106459\t1.52752523165195\t3.05505046330389\n+mz_1200.14\t3.05505046330389\t0\t0.577350269189626\n+mz_1200.18\t0.577350269189626\t3\t2.3094010767585\n+mz_1200.22\t1.52752523165195\t0.577350269189626\t1.52752523165195\n+mz_1200.26\t2.08166599946613\t0.577350269189626\t1.52752523165195\n+mz_1200.3\t1.15470053837925\t1.52752523165195\t1\n+mz_1200.34\t1.52752523165195\t1.15470053837925\t3.05505046330389\n+mz_1200.38\t1.52752523165195\t1.15470053837925\t1.73205080756888\n+mz_1200.42\t2.88675134594813\t1\t3.51188458428425\n+mz_1200.47\t2.64575131106459\t1\t2.08166599946613\n+mz_1200.51\t7.57187779440036\t1.52752523165195\t5.03322295684717\n+mz_1200.55\t15.5884572681199\t2.3094010767585\t3.78593889720018\n+mz_1200.59\t17.0391705588427\t5.19615242270663\t1.52752523165195\n+mz_1200.63\t13\t4.50924975282289\t4.58257569495584\n+mz_1200.67\t8.32666399786453\t1.52752523165195\t1.15470053837925\n+mz_1200.71\t6.35085296108588\t1.52752523165195\t3.21455025366432\n+mz_1200.76\t4.16333199893227\t1.15470053837925\t2\n+mz_1200.8\t2.64575131106459\t1.52752523165195\t1.15470053837925\n+mz_1200.84\t2.3094010767585\t0.577350269189626\t0\n+mz_1200.88\t3.21455025366432\t1.15470053837925\t1.15470053837925\n+mz_1200.92\t2.64575131106459\t2.08166599946613\t2.08166599946613\n+mz_1200.96\t1.73205080756888\t1\t2.3094010767585\n+mz_1201\t1.52752523165195\t1.73205080756888\t1.52752523165195\n+mz_1201.05\t1\t1.15470053837925\t0.577350269189626\n+mz_1201.09\t2.3094010767585\t1.52752523165195\t1.52752523165195\n+mz_1201.13\t1.73205080756888\t0.577350269189626\t2.64575131106459\n+mz_1201.17\t1\t1.52752523165195\t2.64575131106459\n+mz_1201.21\t0.577350269189626\t0.577350269189626\t2.08166599946613\n+mz_1201.25\t1.52752523165195\t0.577350269189626\t0\n+mz_1201.29\t1.52752523165195\t0.577350269189626\t1\n+mz_1201.33\t1.15470053837925\t2.64575131106459\t2.64575131106459\n+mz_1201.38\t2.08166599946613\t1.73205080756888\t1\n+mz_1201.42\t5.13160143944688\t3.78593889720018\t3.05505046330389\n+mz_1201.46\t2.3094010767585\t1.73205080756888\t1.15470053837925\n+mz_1201.5\t6.65832811847939\t0.577350269189626\t2.64575131106459\n+mz_1201.54\t7\t2.51661147842358\t2.64575131106459\n+mz_1201.58\t5.5075705472861\t1.52752523165195\t2\n+mz_1201.62\t3.78593889720018\t1.52752523165195\t2.64575131106459\n+mz_1201.67\t2.64575131106459\t1.52752523165195\t0.577350269189626\n+mz_1201.71\t2.64575131106459\t1\t1.52752523165195\n+mz_1201.75\t3.78593889720018\t1.73205080756888\t1.15470053837925\n+mz_1201.79\t3.21455025366432\t2\t1\n+mz_1201.83\t2.64575131106459\t0\t2.51661147842358\n+mz_1201.87\t1.52752523165195\t0\t1\n+mz_1201.91\t1.52752523165195\t1.15470053837925\t0.577350269189626\n+mz_1201.96\t1\t1.15470053837925\t1.15470053837925\n+mz_1202\t2.64575131106459\t2\t0.577350269189626\n+mz_1202.04\t2.88675134594813\t1\t1\n+mz_1202.08\t2.08166599946613\t1.73205080756888\t1.52752523165195\n+mz_1202.12\t1.15470053837925\t1.52752523165195\t0.577350269189626\n+mz_1202.16\t1\t1\t2.64575131106459\n+mz_1202.2\t2.64575131106459\t1\t1.15470053837925\n+mz_1202.25\t2.08166599946613\t1.52752523165195\t1\n+mz_1202.29\t1\t1.52752523165195\t2\n+mz_1202.33\t3\t1.52752523165195\t1.73205080756888\n+mz_1202.37\t3.78593889720018\t0.577350269189626\t3.60555127546399\n+mz_1202.41\t2.5166114784'..b'523165195\t1\t1.52752523165195\n+mz_1352.74\t1.52752523165195\t1\t2\n+mz_1352.78\t1\t1.52752523165195\t1.52752523165195\n+mz_1352.83\t1\t0.577350269189626\t1.73205080756888\n+mz_1352.87\t1.15470053837925\t1.73205080756888\t0.577350269189626\n+mz_1352.91\t2.08166599946613\t1.52752523165195\t0.577350269189626\n+mz_1352.96\t1.52752523165195\t1.15470053837925\t0.577350269189626\n+mz_1353\t2.08166599946613\t0.577350269189626\t0.577350269189626\n+mz_1353.05\t1.15470053837925\t1.15470053837925\t1.52752523165195\n+mz_1353.09\t1.52752523165195\t2.08166599946613\t0.577350269189626\n+mz_1353.13\t1.52752523165195\t1\t1.73205080756888\n+mz_1353.18\t0.577350269189626\t0.577350269189626\t1.52752523165195\n+mz_1353.22\t1.52752523165195\t0.577350269189626\t1\n+mz_1353.27\t1.52752523165195\t0.577350269189626\t2.88675134594813\n+mz_1353.31\t0.577350269189626\t1.52752523165195\t0\n+mz_1353.35\t3\t2\t1.15470053837925\n+mz_1353.4\t0.577350269189626\t1.15470053837925\t3.60555127546399\n+mz_1353.44\t2\t2.08166599946613\t1\n+mz_1353.48\t1\t1.15470053837925\t1.52752523165195\n+mz_1353.53\t2.3094010767585\t4.04145188432738\t3.51188458428425\n+mz_1353.57\t3\t1.15470053837925\t2.08166599946613\n+mz_1353.62\t1.15470053837925\t3.05505046330389\t2.08166599946613\n+mz_1353.66\t4.16333199893227\t0.577350269189626\t2.64575131106459\n+mz_1353.7\t2.3094010767585\t2.3094010767585\t3.21455025366432\n+mz_1353.75\t1.15470053837925\t1.15470053837925\t1.15470053837925\n+mz_1353.79\t1\t1.15470053837925\t2.08166599946613\n+mz_1353.84\t3.46410161513775\t0.577350269189626\t1\n+mz_1353.88\t1\t2.08166599946613\t1.15470053837925\n+mz_1353.92\t0.577350269189626\t1.15470053837925\t2\n+mz_1353.97\t1\t1.52752523165195\t0.577350269189626\n+mz_1354.01\t0.577350269189626\t0.577350269189626\t2.08166599946613\n+mz_1354.06\t1\t2.08166599946613\t0.577350269189626\n+mz_1354.1\t1\t0.577350269189626\t1.52752523165195\n+mz_1354.14\t0.577350269189626\t1.52752523165195\t0.577350269189626\n+mz_1354.19\t1\t0.577350269189626\t2\n+mz_1354.23\t3.78593889720018\t1\t1.15470053837925\n+mz_1354.28\t0.577350269189626\t1.52752523165195\t0.577350269189626\n+mz_1354.32\t1.52752523165195\t0.577350269189626\t0.577350269189626\n+mz_1354.36\t1\t0.577350269189626\t1.73205080756888\n+mz_1354.41\t2.88675134594813\t1\t2.08166599946613\n+mz_1354.45\t3.21455025366432\t3\t2.3094010767585\n+mz_1354.5\t1\t2.3094010767585\t1\n+mz_1354.54\t3.60555127546399\t2\t3.21455025366432\n+mz_1354.58\t1.73205080756888\t2.08166599946613\t0.577350269189626\n+mz_1354.63\t1.52752523165195\t1.52752523165195\t1\n+mz_1354.67\t2\t2.64575131106459\t1\n+mz_1354.72\t1.15470053837925\t0.577350269189626\t1.15470053837925\n+mz_1354.76\t1.73205080756888\t3.46410161513775\t1\n+mz_1354.8\t1.15470053837925\t1.52752523165195\t0.577350269189626\n+mz_1354.85\t1.15470053837925\t0.577350269189626\t1\n+mz_1354.89\t1.73205080756888\t0.577350269189626\t1\n+mz_1354.93\t2.08166599946613\t0.577350269189626\t0.577350269189626\n+mz_1354.98\t1.52752523165195\t1\t2\n+mz_1355.02\t1.15470053837925\t1\t0.577350269189626\n+mz_1355.07\t0.577350269189626\t2.08166599946613\t0.577350269189626\n+mz_1355.11\t1.15470053837925\t2\t1\n+mz_1355.15\t0.577350269189626\t0\t0.577350269189626\n+mz_1355.2\t0\t1.73205080756888\t1.52752523165195\n+mz_1355.24\t1.15470053837925\t2\t0.577350269189626\n+mz_1355.29\t2\t0.577350269189626\t0.577350269189626\n+mz_1355.33\t1.73205080756888\t0.577350269189626\t2.08166599946613\n+mz_1355.37\t0.577350269189626\t1\t1.15470053837925\n+mz_1355.42\t3.78593889720018\t2.51661147842358\t2.3094010767585\n+mz_1355.46\t3.21455025366432\t3.51188458428425\t1.73205080756888\n+mz_1355.51\t2.51661147842358\t1.52752523165195\t1.52752523165195\n+mz_1355.55\t1\t2.64575131106459\t3.60555127546399\n+mz_1355.59\t1\t1\t3.05505046330389\n+mz_1355.64\t1\t2.08166599946613\t1.52752523165195\n+mz_1355.68\t2.88675134594813\t1\t1\n+mz_1355.73\t2.08166599946613\t0\t4.58257569495584\n+mz_1355.77\t2\t0\t0.577350269189626\n+mz_1355.81\t0.577350269189626\t1\t0.577350269189626\n+mz_1355.86\t1\t1.73205080756888\t1\n+mz_1355.9\t1\t1.73205080756888\t1.15470053837925\n+mz_1355.95\t2.51661147842358\t1\t0.577350269189626\n+mz_1355.99\t1.15470053837925\t1.73205080756888\t1.15470053837925\n+mz_1356.03\t1.73205080756888\t0\t1.52752523165195\n+mz_1356.08\t1.52752523165195\t2.08166599946613\t1\n'

diff -r 000000000000 -r 5f18275c250a 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 01:07:13 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 5f18275c250a 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 01:07:13 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 5f18275c250a test-data/tabular_LM8file16.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_LM8file16.tabular Mon Oct 01 01:07:13 2018 -0400

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

diff -r 000000000000 -r 5f18275c250a test-data/tabular_analyze75.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_analyze75.tabular Mon Oct 01 01:07:13 2018 -0400

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

diff -r 000000000000 -r 5f18275c250a test-data/tabular_imzml.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_imzml.tabular Mon Oct 01 01:07:13 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 5f18275c250a test-data/tabular_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_rdata.tabular Mon Oct 01 01:07:13 2018 -0400

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

diff -r 000000000000 -r 5f18275c250a test-data/test1.pdf

Binary file test-data/test1.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test2.pdf

Binary file test-data/test2.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test2.rdata

Binary file test-data/test2.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/test3.pdf

Binary file test-data/test3.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test4.pdf

Binary file test-data/test4.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test4.rdata

Binary file test-data/test4.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/test5.pdf

Binary file test-data/test5.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test6.pdf

Binary file test-data/test6.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test6.rdata

Binary file test-data/test6.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/test7.pdf

Binary file test-data/test7.pdf has changed

diff -r 000000000000 -r 5f18275c250a test-data/test7.rdata

Binary file test-data/test7.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/testfile_squares.rdata

Binary file test-data/testfile_squares.rdata has changed

diff -r 000000000000 -r 5f18275c250a test-data/toplabels_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_skm.tabular Mon Oct 01 01:07:13 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 5f18275c250a test-data/toplabels_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_ssc.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,51 @@
+mz r k s classes centers tstatistics p.values adj.p.values
+364.333343505859 1 3 2 1 15.8337765722821 0.449479909587349 NA NA
+364.333343505859 2 3 2 1 15.8337765722821 0.449479909587349 NA NA
+203.833343505859 1 3 2 1 14.0415253451331 0.449478654505296 NA NA
+203.833343505859 2 3 2 1 14.0415253451331 0.449478654505296 NA NA
+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
+360.916687011719 2 3 2 1 9.04224883162212 0.449472524177856 NA NA
+370.083343505859 1 3 2 1 8.45643021892373 0.44947133139287 NA NA
+370.083343505859 2 3 2 1 8.45643021892373 0.44947133139287 NA NA
+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
+249.25 2 3 2 1 5.15263210866428 0.449459526788925 NA NA
+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 5f18275c250a test-data/xy_coordinates.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates.tabular Mon Oct 01 01:07:13 2018 -0400

@@ -0,0 +1,3 @@
+0 0 File1
+1 0 File2
+6 0 File3