Repository 'cardinal_mz_images'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images

Changeset 0:2ba12c97f7cc (2018-10-01)
Next changeset 1:4d5f798a7a18 (2018-10-25)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
added:
macros.xml
mz_images.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
b
diff -r 000000000000 -r 2ba12c97f7cc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 01 01:06:41 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'
b
diff -r 000000000000 -r 2ba12c97f7cc mz_images.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mz_images.xml Mon Oct 01 01:06:41 2018 -0400
[
b'@@ -0,0 +1,229 @@\n+<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0">\n+    <description>\n+        mass spectrometry imaging m/z heatmaps\n+    </description>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <expand macro="requirements">\n+        <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+        <requirement type="package" version="0.20-35">r-lattice</requirement>\n+    </expand>\n+    <command detect_errors="aggressive">\n+<![CDATA[\n+        @INPUT_LINKING@\n+        cat \'${MSI_heatmaps}\' &&\n+        Rscript \'${MSI_heatmaps}\'\n+]]>\n+    </command>\n+    <configfiles>\n+        <configfile name="MSI_heatmaps"><![CDATA[\n+\n+################################# load libraries and read file #################\n+\n+library(Cardinal)\n+library(gridExtra)\n+library(lattice)\n+\n+@READING_MSIDATA@\n+\n+@DATA_PROPERTIES@\n+\n+##################################### read and filter input m/z ##############\n+\n+input_list = read.delim("$calibrant_file", header = $calibrant_header, stringsAsFactors = FALSE)\n+input_list = input_list[,c($mz_column, $name_column)]\n+\n+### calculate how many input m/z are valid: \n+inputmasses = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]\n+inputmz = as.numeric(inputmasses[,1])\n+inputnames = as.character(inputmasses[,2])\n+\n+\n+############################## PDF #############################################\n+################################################################################\n+\n+pdf("heatmaps.pdf", fonts = "Times", pointsize = 12)\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n+#if not $filename:\n+    #set $filename = $infile.display_name\n+#end if\n+title(main=paste("\\nHeatmap images\\n\\n", "Filename:\\n", "$filename"))\n+\n+new_row = data.frame(paste0(length(inputmz), "/", length(input_list[,1])), paste0("# valid m/z in \\n", "$calibrant_file.display_name"))\n+colnames(new_row) = c("properties", "values")\n+property_df = rbind(property_df, new_row)\n+\n+grid.table(property_df, rows= NULL)\n+\n+############################# II) images ####################################\n+\n+### only plot images when file has peaks and valid input m/z: \n+\n+if (npeaks > 0){\n+    if (length(inputmz) != 0){\n+        for (mass in 1:length(inputmz)){\n+\n+            ###standard image\n+\n+            #if str($image_type) == "standard_image":\n+                print("standard image")\n+\n+                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", \n+                smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),\n+                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n+\n+\n+            ###lattice image\n+\n+            #elif str($image_type) == "lattice_image":\n+                print("lattice image")\n+\n+                #if str($strip) =="TRUE": \n+\n+                print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),\n+                lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", \n+                colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),\n+                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n+\n+                #elif str($strip) =="FALSE": \n+\n+                print(image(msidata, mz=inputmz[mass], strip = $strip,\n+                lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", \n+                colorkey=$colorkey,\n+                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," \xc2\xb1 ", $plusminus_dalton, " Da)")))}\n+\n+                #end if\n+\n+            #end if \n+\n+        ## optional svg output with original coordinates\n+        #if $svg_pixelimage:\n+            pri'..b'/data>\n+    </outputs>\n+    <tests>\n+        <test>\n+            <expand macro="infile_imzml"/>\n+            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>\n+            <param name="mz_column" value="1"/>\n+            <param name="name_column" value="2"/>\n+            <param name="plusminus_dalton" value="0.25"/>\n+            <param name="filename" value="Testfile_imzml"/>\n+            <param name="image_contrast" value="histogram"/>\n+            <param name="strip" value="True"/>\n+            <param name="colorkey" value="True"/>\n+            <param name="image_type" value="lattice_image"/>\n+            <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/>\n+        </test>\n+        <test>\n+            <expand macro="infile_analyze75"/>\n+            <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>\n+            <param name="mz_column" value="1"/>\n+            <param name="name_column" value="1"/>\n+            <param name="plusminus_dalton" value="0.5"/>\n+            <param name="filename" value="Testfile_analyze75"/>\n+            <param name="image_smoothing" value="gaussian"/>\n+            <param name="strip" value="False"/>\n+            <param name="colorkey" value="True"/>\n+            <param name="svg_pixelimage" value="True"/>\n+            <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>\n+            <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>\n+        </test>\n+        <test>\n+            <param name="infile" value="preprocessed.rdata" ftype="rdata"/>\n+            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>\n+            <param name="mz_column" value="1"/>\n+            <param name="name_column" value="2"/>\n+            <param name="plusminus_dalton" value="0.5"/>\n+            <param name="strip" value="True"/>\n+            <param name="colorkey" value="True"/>\n+            <param name="image_type" value="lattice_image"/>\n+            <param name="filename" value="Testfile_rdata"/>\n+            <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/>\n+        </test>\n+        <test>\n+            <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>\n+            <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>\n+            <param name="mz_column" value="1"/>\n+            <param name="name_column" value="1"/>\n+            <param name="plusminus_dalton" value="0.5"/>\n+            <param name="strip" value="True"/>\n+            <param name="colorkey" value="False"/>\n+            <param name="filename" value="Testfile_rdata"/>\n+            <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+\n+\n+@CARDINAL_DESCRIPTION@\n+\n+-----\n+\n+This tool uses the Cardinal image function to plot the intensity distribution of m/z feature of mass spectrometry imaging data. \n+\n+@MSIDATA_INPUT_DESCRIPTION@\n+\n+@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@\n+\n+**Tips** \n+\n+- In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))\n+- No heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0 or all chosen m/z features are not present in the MSI dataset\n+- The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra\n+- The standard image function should work for all files while the lattice function works not perfectly on every file\n+\n+**Output**\n+\n+- Pdf with the heatmap images\n+- optional: svg file with the heatmap of the first valid m/z in the tabular file\n+\n+\n+    ]]>\n+    </help>\n+    <expand macro="citations"/>\n+</tool>\n'
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/112_auto_combined.RData
b
Binary file test-data/112_auto_combined.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/112_auto_combined_QC.pdf
b
Binary file test-data/112_auto_combined_QC.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/123_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/123_combined.RData
b
Binary file test-data/123_combined.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/123_combined_QC.pdf
b
Binary file test-data/123_combined_QC.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/12_combined.RData
b
Binary file test-data/12_combined.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/12_combined_QC.pdf
b
Binary file test-data/12_combined_QC.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/2123_auto_combined.RData
b
Binary file test-data/2123_auto_combined.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/2123_auto_combined_QC.pdf
b
Binary file test-data/2123_auto_combined_QC.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/3_files_combined.RData
b
Binary file test-data/3_files_combined.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Analyze75.hdr
b
Binary file test-data/Analyze75.hdr has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Analyze75.img
b
Binary file test-data/Analyze75.img has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Analyze75.t2m
b
Binary file test-data/Analyze75.t2m has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Example_Continuous.ibd
b
Binary file test-data/Example_Continuous.ibd has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Example_Continuous.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Continuous.imzML Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Example_Processed.ibd
b
Binary file test-data/Example_Processed.ibd has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Example_Processed.imzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Processed.imzML Mon Oct 01 01:06:41 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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Heatmaps_LM8_file16.pdf
b
Binary file test-data/Heatmaps_LM8_file16.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Heatmaps_analyze75.pdf
b
Binary file test-data/Heatmaps_analyze75.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Heatmaps_imzml.pdf
b
Binary file test-data/Heatmaps_imzml.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Heatmaps_rdata.pdf
b
Binary file test-data/Heatmaps_rdata.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Plot_analyze75.pdf
b
Binary file test-data/Plot_analyze75.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Plot_analyze75_allpixels.pdf
b
Binary file test-data/Plot_analyze75_allpixels.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Plot_empty_spectra.pdf
b
Binary file test-data/Plot_empty_spectra.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Plot_imzml.pdf
b
Binary file test-data/Plot_imzml.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/Plot_rdata.pdf
b
Binary file test-data/Plot_rdata.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/QC_analyze75.pdf
b
Binary file test-data/QC_analyze75.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/QC_empty_spectra.pdf
b
Binary file test-data/QC_empty_spectra.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/QC_imzml.pdf
b
Binary file test-data/QC_imzml.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/QC_rdata.pdf
b
Binary file test-data/QC_rdata.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze75.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/analyze75.svg Mon Oct 01 01:06:41 2018 -0400
b
@@ -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>
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze75_filtered2.pdf
b
Binary file test-data/analyze75_filtered2.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze_filtered.RData
b
Binary file test-data/analyze_filtered.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze_filtered.pdf
b
Binary file test-data/analyze_filtered.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze_filteredoutside.RData
b
Binary file test-data/analyze_filteredoutside.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze_originaloutput.RData
b
Binary file test-data/analyze_originaloutput.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/analyze_originaloutput2.RData
b
Binary file test-data/analyze_originaloutput2.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/annotations.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/annotations_file1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file1.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/annotations_file2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file2.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/annotations_file3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_file3.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/annotations_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotations_rdata.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/centroids_rdata.pdf
b
Binary file test-data/centroids_rdata.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/classes_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/classes_ssc.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/cluster_skm.RData
b
Binary file test-data/cluster_skm.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/cluster_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster_skm.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/empty_spectra.rdata
b
Binary file test-data/empty_spectra.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out1.tabular Mon Oct 01 01:06:41 2018 -0400
b
b'@@ -0,0 +1,1200 @@\n+mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n+mz_300.08\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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out3.tabular Mon Oct 01 01:06:41 2018 -0400
b
b'@@ -0,0 +1,1200 @@\n+mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n+mz_300.08\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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test2.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test4.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test6.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/features_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_test7.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/featuresofinterest5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featuresofinterest5.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,31 @@
+115.333335876465
+115.416664123535
+115.5
+115.583335876465
+115.666664123535
+115.75
+115.833335876465
+115.916664123535
+116
+116.083335876465
+116.166664123535
+116.25
+116.333335876465
+116.416664123535
+116.5
+116.583335876465
+116.666664123535
+319.083343505859
+319.166687011719
+319.25
+319.333343505859
+319.416687011719
+319.5
+319.583343505859
+319.666687011719
+319.75
+319.8
+319.916687011719
+320
+320.0833435
+350
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered.RData
b
Binary file test-data/imzml_filtered.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered.pdf
b
Binary file test-data/imzml_filtered.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered2.pdf
b
Binary file test-data/imzml_filtered2.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered3.RData
b
Binary file test-data/imzml_filtered3.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered3.pdf
b
Binary file test-data/imzml_filtered3.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered4.RData
b
Binary file test-data/imzml_filtered4.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered4.pdf
b
Binary file test-data/imzml_filtered4.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered5.RData
b
Binary file test-data/imzml_filtered5.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/imzml_filtered5.pdf
b
Binary file test-data/imzml_filtered5.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/inputcalibrantfile1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile1.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,3 @@
+101.5
+356.7
+555.1
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/inputcalibrantfile2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputcalibrantfile2.txt Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,3 @@
+869.51 mass1
+1111.1 mass2
+1296.7 mass3
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/inputpeptides.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,3 @@
+152 mass1
+328.9 mass2
+185.2 mass3
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/inputpeptides2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpeptides2.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,4 @@
+854.5
+1111.1
+1296.7
+1305.1
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/inputpixels_2column.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputpixels_2column.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,6 @@
+1 A 1
+1 B 2
+1 C 3
+3 D 1
+3 E 2
+30 F 3
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/int_matrix1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix1.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/int_matrix3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int_matrix3.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/kmeans_analyze.pdf
b
Binary file test-data/kmeans_analyze.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/loadings_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loadings_pca.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/mean_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mean_out2.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/msidata_1.RData
b
Binary file test-data/msidata_1.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/msidata_2.RData
b
Binary file test-data/msidata_2.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/msidata_3.RData
b
Binary file test-data/msidata_3.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pca_imzml.pdf
b
Binary file test-data/pca_imzml.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixel_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out2.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixel_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out3.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixels_test2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test2.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixels_test4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test4.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixels_test6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test6.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/pixels_test7.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixels_test7.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessed.RData
b
Binary file test-data/preprocessed.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessed.rdata
b
Binary file test-data/preprocessed.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results1.RData
b
Binary file test-data/preprocessing_results1.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results1.pdf
b
Binary file test-data/preprocessing_results1.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.txt Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results2.RData
b
Binary file test-data/preprocessing_results2.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results2.pdf
b
Binary file test-data/preprocessing_results2.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.txt Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results3.RData
b
Binary file test-data/preprocessing_results3.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results3.pdf
b
Binary file test-data/preprocessing_results3.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results4.RData
b
Binary file test-data/preprocessing_results4.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results4.pdf
b
Binary file test-data/preprocessing_results4.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results4.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.txt Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results5.RData
b
Binary file test-data/preprocessing_results5.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results5.pdf
b
Binary file test-data/preprocessing_results5.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/preprocessing_results5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.txt Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/random_factors.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_factors.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,24 @@
+1 1 f1 A
+2 1 f1 A
+3 1 f2 B
+4 1 f1 C
+1 2 f2 C
+2 2 f2 C
+3 2 f2 B
+4 2 f2 A
+1 3 f2 A
+2 3 f1 B
+3 3 f2 C
+4 3 f1 A
+10 1 f1 A
+11 1 f2 C
+12 1 f1 B
+13 1 f1 B
+10 2 f1 B
+11 2 f1 A
+12 2 f2 C
+13 2 f2 A
+10 3 f1 C
+11 3 f2 B
+12 3 f1 B
+13 3 f2 C
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/rdata_notfiltered.RData
b
Binary file test-data/rdata_notfiltered.RData has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/rdata_notfiltered.pdf
b
Binary file test-data/rdata_notfiltered.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/scores_pca.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scores_pca.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/sd_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sd_out2.tabular Mon Oct 01 01:06:41 2018 -0400
b
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'
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc 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 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/tabular_LM8file16.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_LM8file16.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,2 @@
+inputmz countpixels percentpixels
+1111.1 0 0
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/tabular_analyze75.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_analyze75.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,3 @@
+inputmz countpixels percentpixels
+1296.7 9 100
+1305.1 9 100
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/tabular_imzml.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_imzml.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,4 @@
+inputmz countpixels percentpixels
+152 9 100
+328.9 9 100
+185.2 6 66.7
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/tabular_rdata.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabular_rdata.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,2 @@
+inputmz countpixels percentpixels
+328.9 9 100
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test1.pdf
b
Binary file test-data/test1.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test2.pdf
b
Binary file test-data/test2.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test2.rdata
b
Binary file test-data/test2.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test3.pdf
b
Binary file test-data/test3.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test4.pdf
b
Binary file test-data/test4.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test4.rdata
b
Binary file test-data/test4.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test5.pdf
b
Binary file test-data/test5.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test6.pdf
b
Binary file test-data/test6.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test6.rdata
b
Binary file test-data/test6.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test7.pdf
b
Binary file test-data/test7.pdf has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/test7.rdata
b
Binary file test-data/test7.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/testfile_squares.rdata
b
Binary file test-data/testfile_squares.rdata has changed
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/toplabels_skm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_skm.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/toplabels_ssc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_ssc.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -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
b
diff -r 000000000000 -r 2ba12c97f7cc test-data/xy_coordinates.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates.tabular Mon Oct 01 01:06:41 2018 -0400
b
@@ -0,0 +1,3 @@
+0 0 File1
+1 0 File2
+6 0 File3