| Next changeset 1:d4158c9955ea (2018-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_segmentation commit da5a0723327f7cce689b230ccd69f3edecb1bc6b |
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added:
segmentation_tool.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/centroids_imzml.pdf test-data/classes_results1.txt test-data/cluster_results1.txt test-data/kmeans_imzml.pdf test-data/pca_imzml.pdf test-data/pcaloadings_results1.txt test-data/pcascores_results1.txt test-data/preprocessing_results1.RData test-data/toplabels_results1.txt |
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| diff -r 000000000000 -r 0c1a9b68f436 segmentation_tool.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentation_tool.xml Sat Feb 24 13:51:32 2018 -0500 |
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| b'@@ -0,0 +1,409 @@\n+<tool id="mass_spectrometry_imaging_segmentations" name="MSI segmentation" version="1.7.0">\n+ <description>tool for spatial clustering</description>\n+ <requirements>\n+ <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>\n+ <requirement type="package" version="2.2.1">r-gridextra</requirement>\n+ <requirement type="package" version="2.23-15">r-kernsmooth</requirement>\n+ <requirement type="package" version="0.20-35">r-lattice</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ #if $infile.ext == \'imzml\'\n+ cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ #elif $infile.ext == \'analyze75\'\n+ cp \'${infile.extra_files_path}/hdr\' infile.hdr &&\n+ cp \'${infile.extra_files_path}/img\' infile.img &&\n+ cp \'${infile.extra_files_path}/t2m\' infile.t2m &&\n+ #else\n+ ln -s $infile infile.RData &&\n+ #end if\n+ cat \'${MSI_segmentation}\' &&\n+ echo ${MSI_segmentation} &&\n+ Rscript \'${MSI_segmentation}\'\n+\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="MSI_segmentation"><![CDATA[\n+\n+\n+################################# load libraries and read file #########################\n+\n+\n+library(Cardinal)\n+library(gridExtra)\n+library(KernSmooth)\n+library(lattice)\n+\n+## Read MALDI Imaging dataset\n+\n+#if $infile.ext == \'imzml\'\n+ msidata <- readMSIData(\'infile.imzML\')\n+#elif $infile.ext == \'analyze75\'\n+ msidata <- readMSIData(\'infile.hdr\')\n+#else\n+ load(\'infile.RData\')\n+#end if\n+\n+###################################### file properties in numbers ######################\n+\n+## Number of features (mz)\n+maxfeatures = length(features(msidata))\n+## Range mz\n+minmz = round(min(mz(msidata)), digits=2)\n+maxmz = round(max(mz(msidata)), digits=2)\n+## Number of spectra (pixels)\n+pixelcount = length(pixels(msidata))\n+## Range x coordinates\n+minimumx = min(coord(msidata)[,1])\n+maximumx = max(coord(msidata)[,1])\n+## Range y coordinates\n+minimumy = min(coord(msidata)[,2])\n+maximumy = max(coord(msidata)[,2])\n+## Range of intensities\n+minint = round(min(spectra(msidata)[]), digits=2)\n+maxint = round(max(spectra(msidata)[]), digits=2)\n+medint = round(median(spectra(msidata)[]), digits=2)\n+## Number of intensities > 0\n+npeaks= sum(spectra(msidata)[]>0)\n+## Spectra multiplied with mz (potential number of peaks)\n+numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n+## Percentage of intensities > 0\n+percpeaks = round(npeaks/numpeaks*100, digits=2)\n+## Number of empty TICs\n+TICs = colSums(spectra(msidata)[]) \n+NumemptyTIC = sum(TICs == 0)\n+\n+\n+## Processing informations\n+processinginfo = processingData(msidata)\n+centroidedinfo = processinginfo@centroided # TRUE or FALSE\n+\n+## if TRUE write processinginfo if no write FALSE\n+\n+## normalization\n+if (length(processinginfo@normalization) == 0) {\n+ normalizationinfo=\'FALSE\'\n+} else {\n+ normalizationinfo=processinginfo@normalization\n+}\n+## smoothing\n+if (length(processinginfo@smoothing) == 0) {\n+ smoothinginfo=\'FALSE\'\n+} else {\n+ smoothinginfo=processinginfo@smoothing\n+}\n+## baseline\n+if (length(processinginfo@baselineReduction) == 0) {\n+ baselinereductioninfo=\'FALSE\'\n+} else {\n+ baselinereductioninfo=processinginfo@baselineReduction\n+}\n+## peak picking\n+if (length(processinginfo@peakPicking) == 0) {\n+ peakpickinginfo=\'FALSE\'\n+} else {\n+ peakpickinginfo=processinginfo@peakPicking\n+}\n+\n+#############################################################################\n+\n+properties = c("Number of mz features",\n+ "Range of mz values [Da]",\n+ "Number of pixels", \n+ "Range of x coordinates", \n+ "Range of y coordinates",\n+ "Range of intensities", \n+ "Median of intensities",\n+ "Intensities > 0",\n+ "Number of ze'..b'me} on $infile.display_name"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Continuous.imzML"/>\n+ <composite_data value="Example_Continuous.ibd"/>\n+ </param>\n+ <param name="segmentationtool" value="pca"/>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#ff00ff"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#0000FF"/>\n+ </repeat>\n+ <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size" delta="20000"/>\n+ <output name="mzfeatures" file="pcaloadings_results1.txt" compare="sim_size"/>\n+ <output name="pixeloutput" file="pcascores_results1.txt" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="" ftype="analyze75">\n+ <composite_data value="Analyze75.hdr" />\n+ <composite_data value="Analyze75.img" />\n+ <composite_data value="Analyze75.t2m" />\n+ </param>\n+ <param name="segmentationtool" value="kmeans"/>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#ff00ff"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#0000FF"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#00C957"/>\n+ </repeat>\n+ <output name="segmentationimages" file="kmeans_imzml.pdf" compare="sim_size" delta="20000"/>\n+ <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/>\n+ <output name="pixeloutput" file="cluster_results1.txt" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <param name="segmentationtool" value="centroids"/>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#0000FF"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#00C957"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#B0171F"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#FFD700"/>\n+ </repeat>\n+ <repeat name="colours">\n+ <param name="feature_color" value="#848484"/>\n+ </repeat>\n+ <output name="segmentationimages" file="centroids_imzml.pdf" compare="sim_size" delta="20000"/>\n+ <output name="mzfeatures" file="toplabels_results1.txt" compare="sim_size"/>\n+ <output name="pixeloutput" file="classes_results1.txt" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+Spatially aware segmentation of mass-spectrometry imaging data by unsupervised clustering algorithms. Underlying structures can be identified with the following tools: pca, k-means clustering and spatial shrunken centroids. The spatialShrunkenCentroids method allows the number of segments to decrease according to the data. This allows automatic selection of the number\n+of clusters.\n+\n+Input data: 3 types of input data can be used:\n+\n+- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_\n+- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)\n+- Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)\n+\n+The output of this tool contains a pdf with plots from the segmentation tools. \n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 0c1a9b68f436 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Sat Feb 24 13:51:32 2018 -0500 |
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| 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="{554A27FA-79D2-4766-9A2C-862E6D78B1F3}"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="A5BE532D25997B71BE6D20C76561DDC4D5307DDD"/>\r\n+ <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" 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't" value="16"/>\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="235188"/>\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="16"/>\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="268784"/>\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="16"/>\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="302380"/>\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' |
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| diff -r 000000000000 -r 0c1a9b68f436 test-data/classes_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/classes_results1.txt Sat Feb 24 13:51:32 2018 -0500 |
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| @@ -0,0 +1,10 @@ + x +x = 1, y = 1 1 +x = 2, y = 1 1 +x = 3, y = 1 1 +x = 1, y = 2 1 +x = 2, y = 2 1 +x = 3, y = 2 1 +x = 1, y = 3 1 +x = 2, y = 3 1 +x = 3, y = 3 1 |
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| diff -r 000000000000 -r 0c1a9b68f436 test-data/cluster_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_results1.txt Sat Feb 24 13:51:32 2018 -0500 |
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| @@ -0,0 +1,10 @@ + x +x = 1, y = 1 3 +x = 2, y = 1 2 +x = 3, y = 1 2 +x = 1, y = 2 2 +x = 2, y = 2 2 +x = 3, y = 2 2 +x = 1, y = 3 1 +x = 2, y = 3 2 +x = 3, y = 3 2 |
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| diff -r 000000000000 -r 0c1a9b68f436 test-data/pcaloadings_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pcaloadings_results1.txt Sat Feb 24 13:51:32 2018 -0500 |
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| b'@@ -0,0 +1,8400 @@\n+\tPC1\tPC2\n+m/z = 100.08\t-1.86059990031193e-19\t-4.20095088814001e-19\n+m/z = 100.17\t9.87509444691618e-20\t2.35147879854537e-19\n+m/z = 100.25\t1.09097027695743e-19\t2.4228535983709e-19\n+m/z = 100.33\t-2.08830496743711e-20\t-4.85115687658163e-20\n+m/z = 100.42\t3.15093935579793e-19\t7.61345646065437e-19\n+m/z = 100.5\t4.73643315429366e-20\t1.16213766542198e-19\n+m/z = 100.58\t-0.000104656106492356\t0.000353453375099747\n+m/z = 100.67\t-0.00191806412960808\t0.00647784695026133\n+m/z = 100.75\t-0.00180844223665621\t0.00610762270489929\n+m/z = 100.83\t0.000360645067163725\t0.00196796460781247\n+m/z = 100.92\t0.0149012861337974\t0.00227595239712752\n+m/z = 101\t0.0175435591487301\t-0.0143023652391706\n+m/z = 101.08\t0.031002747135816\t0.0122614203884688\n+m/z = 101.17\t0.0338611449231094\t0.0223356162474473\n+m/z = 101.25\t0.00673689843629034\t0.00469328645894403\n+m/z = 101.33\t-6.07248591968159e-06\t-7.65206415618305e-07\n+m/z = 101.42\t-8.72856050015876e-09\t2.94788261457765e-08\n+m/z = 101.5\t3.45834782552111e-07\t-1.20261345070239e-06\n+m/z = 101.58\t3.23622451834405e-07\t-1.12537180515533e-06\n+m/z = 101.67\t3.8611747847706e-06\t2.37941054624083e-06\n+m/z = 101.75\t1.16030815032252e-06\t8.0438871071427e-07\n+m/z = 101.83\t1.00752913826984e-07\t7.12295619845451e-08\n+m/z = 101.92\t-1.83947711227944e-12\t6.21243627026478e-12\n+m/z = 102\t-4.17258893310736e-14\t1.40918554344855e-13\n+m/z = 102.08\t3.30267002709013e-11\t-1.14847768724187e-10\n+m/z = 102.17\t2.71286069592646e-10\t1.38524371581216e-10\n+m/z = 102.25\t1.61761087755614e-10\t1.07254853863827e-10\n+m/z = 102.33\t2.76943739547824e-11\t1.93156959489091e-11\n+m/z = 102.42\t-2.92749887941464e-16\t9.86940330694681e-16\n+m/z = 102.5\t-3.4051403301236e-17\t1.14403988503004e-16\n+m/z = 102.58\t2.02823230444141e-15\t-7.05332921030856e-15\n+m/z = 102.67\t1.46068550491091e-15\t-5.08048086214669e-15\n+m/z = 102.75\t1.81356277671187e-14\t1.13406889067328e-14\n+m/z = 102.83\t4.99459890522449e-15\t3.46465652724235e-15\n+m/z = 102.92\t3.54654620472745e-16\t2.52101917234947e-16\n+m/z = 103\t-7.33633722360385e-20\t-1.20274920856386e-19\n+m/z = 103.08\t1.41618326920922e-19\t3.72875524743884e-19\n+m/z = 103.17\t-2.19975190398912e-19\t-1.43359941267792e-18\n+m/z = 103.25\t1.42891908175342e-18\t7.88710114358005e-19\n+m/z = 103.33\t6.41297597138591e-19\t2.78255342751776e-19\n+m/z = 103.42\t8.46894101356055e-20\t1.65833163524832e-20\n+m/z = 103.5\t-1.50221528863782e-19\t-3.58744763503543e-19\n+m/z = 103.58\t-1.82850015700516e-19\t-4.2644833675042e-19\n+m/z = 103.67\t-1.84122111338174e-19\t-4.38571120486911e-19\n+m/z = 103.75\t-9.30780295318121e-21\t-2.3520100648106e-20\n+m/z = 103.83\t-1.65598948043249e-19\t-4.22198345569072e-19\n+m/z = 103.92\t-6.85264194378445e-20\t-1.6350267764531e-19\n+m/z = 104\t2.54015057897185e-19\t6.10979475376383e-19\n+m/z = 104.08\t-2.73920283032827e-20\t-6.21437335507252e-20\n+m/z = 104.17\t-2.58053385535497e-19\t-6.04029115522955e-19\n+m/z = 104.25\t4.75925321388198e-20\t1.09512432077898e-19\n+m/z = 104.33\t-3.75580297011702e-20\t-8.36745295564117e-20\n+m/z = 104.42\t-2.12364245926505e-19\t-4.94251798114715e-19\n+m/z = 104.5\t-5.31202059801377e-20\t-1.25121350810266e-19\n+m/z = 104.58\t2.22992656193459e-19\t5.07814577079916e-19\n+m/z = 104.67\t1.54152506561108e-19\t3.75142976244701e-19\n+m/z = 104.75\t4.89928677667099e-22\t1.22217765622567e-21\n+m/z = 104.83\t-8.33910883636569e-20\t-1.87553590799543e-19\n+m/z = 104.92\t3.97572052143163e-19\t9.09541583209455e-19\n+m/z = 105\t-1.60052339088906e-20\t-3.72476803115141e-20\n+m/z = 105.08\t-5.78938586011886e-19\t-1.244036263573e-18\n+m/z = 105.17\t2.30372523518939e-19\t5.47162607642138e-19\n+m/z = 105.25\t-1.1729116805124e-19\t-2.74476091908414e-19\n+m/z = 105.33\t2.7177988163347e-19\t6.01578056987235e-19\n+m/z = 105.42\t-2.81678455627353e-19\t-5.89635523196556e-19\n+m/z = 105.5\t1.1333783354223e-19\t2.35283579480262e-19\n+m/z = 105.58\t-2.73342047052725e-19\t-6.47903025224876e-19\n+m/z = 105.67\t-2.51516708177392e-19\t-6.02295018812391e-19\n+m/z = 105.75\t1.50419796039407e-19\t3.46882189159088e-19\n+m/z = 105.83\t3.12785438881079e-19\t7.77753325844277e-19\n+m/z = 105.92\t-4.27089286960678e-19\t-1.0002810'..b'\n+m/z = 794.08\t-1.02067038586458e-07\t-1.45258975024606e-07\n+m/z = 794.17\t-1.12379272165959e-08\t-1.59935059494185e-08\n+m/z = 794.25\t-1.79445928966385e-19\t-4.00703216842676e-19\n+m/z = 794.33\t1.76267271134409e-19\t4.56914921805518e-19\n+m/z = 794.42\t2.17003145239192e-19\t5.24137377545813e-19\n+m/z = 794.5\t-4.21250006381354e-20\t-9.94030493712647e-20\n+m/z = 794.58\t-0.00477541680078601\t-0.00754050838457741\n+m/z = 794.67\t0.00457278398695885\t-0.0426132474217616\n+m/z = 794.75\t0.00833966396316635\t-0.0346155215563303\n+m/z = 794.83\t0.000966644754810597\t-0.00353481494848323\n+m/z = 794.92\t-0.00195096214440753\t0.00658284942421867\n+m/z = 795\t-0.000640470913415029\t0.00216305205292817\n+m/z = 795.08\t-5.99410062227027e-05\t0.000202437790458378\n+m/z = 795.17\t-5.4014014389065e-07\t-7.68712453672831e-07\n+m/z = 795.25\t7.01767360337984e-07\t-3.35591597300961e-06\n+m/z = 795.33\t3.18791439545021e-07\t-1.2061242591259e-06\n+m/z = 795.42\t-8.91159484677643e-08\t2.9688619163037e-07\n+m/z = 795.5\t-8.7318875313056e-08\t2.94900624757305e-07\n+m/z = 795.58\t-1.56512048740352e-08\t5.28585609798675e-08\n+m/z = 795.67\t-3.01232741113653e-11\t-4.28706071552815e-11\n+m/z = 795.75\t1.48510028562637e-11\t-1.72677973322058e-10\n+m/z = 795.83\t3.8506092534405e-11\t-1.57275897191402e-10\n+m/z = 795.92\t9.04270346863403e-12\t-3.1445297664552e-11\n+m/z = 796\t-9.44016302806483e-12\t3.187448742336e-11\n+m/z = 796.08\t-2.76488416961386e-12\t9.33779840109984e-12\n+m/z = 796.17\t-2.15724645944791e-13\t7.28562321344289e-13\n+m/z = 796.25\t-2.58221231300034e-15\t-3.67492240117948e-15\n+m/z = 796.33\t3.49525520050498e-15\t-1.61257132943202e-14\n+m/z = 796.42\t1.40468494659126e-15\t-5.24764603502545e-15\n+m/z = 796.5\t-5.43139987078557e-16\t1.81732754308213e-15\n+m/z = 796.58\t-3.90875838968025e-16\t1.31905830414735e-15\n+m/z = 796.67\t-0.0111966558774574\t-0.00184642752951266\n+m/z = 796.75\t-0.00616492950080404\t-0.0010166513709427\n+m/z = 796.83\t-0.000947322559573778\t-0.000156221864141355\n+m/z = 796.92\t4.11662469614298e-19\t-1.3216270704391e-19\n+m/z = 797\t-2.17759482515273e-19\t-7.43488309644877e-19\n+m/z = 797.08\t1.79350141189194e-19\t7.44535109941237e-19\n+m/z = 797.17\t-6.18529780126893e-08\t-1.0200102837658e-08\n+m/z = 797.25\t-7.22222614326598e-07\t-1.19100893349065e-07\n+m/z = 797.33\t-1.818942227306e-07\t-2.99959652232607e-08\n+m/z = 797.42\t-9.21039873681872e-09\t-1.51887616891841e-09\n+m/z = 797.5\t6.69667341120041e-20\t1.59012431693488e-19\n+m/z = 797.58\t1.66103283550513e-19\t3.93901432945403e-19\n+m/z = 797.67\t-1.36211415086825e-19\t-2.97929530446326e-19\n+m/z = 797.75\t-6.19645961970517e-11\t-1.02185086744297e-11\n+m/z = 797.83\t-2.72928150794626e-11\t-4.50082713427092e-12\n+m/z = 797.92\t-0.00389097733292416\t-0.00553753088718729\n+m/z = 798\t-0.00407514724498002\t-0.00579963639658733\n+m/z = 798.08\t-0.000963732393772135\t-0.00137155718100157\n+m/z = 798.17\t-3.59243592475192e-05\t-5.11265505001433e-05\n+m/z = 798.25\t-1.58505824753274e-15\t-2.62341211169423e-16\n+m/z = 798.33\t-3.32795606248157e-15\t-5.4914371746535e-16\n+m/z = 798.42\t-7.70622667488165e-16\t-1.2671683736167e-16\n+m/z = 798.5\t-3.69626374554309e-07\t-5.26041992105907e-07\n+m/z = 798.58\t5.18525840962871e-05\t-0.000407429722098979\n+m/z = 798.67\t0.0037464533593935\t-0.0293383545235394\n+m/z = 798.75\t0.00291920523455579\t-0.0228600645485012\n+m/z = 798.83\t0.000533036946002732\t-0.00417417002686781\n+m/z = 798.92\t-2.12094854281441e-19\t-2.42407615253506e-19\n+m/z = 799\t-1.39504211917673e-11\t-1.98538524645768e-11\n+m/z = 799.08\t-1.8662042267273e-11\t-2.65593005367568e-11\n+m/z = 799.17\t-4.06033618452523e-12\t-5.77855774543026e-12\n+m/z = 799.25\t3.15016300887783e-07\t-2.46686834032146e-06\n+m/z = 799.33\t9.32606479023616e-08\t-7.30316733349191e-07\n+m/z = 799.42\t7.58575172019168e-09\t-5.94034197795049e-08\n+m/z = 799.5\t6.19356981829876e-20\t1.45261958914268e-19\n+m/z = 799.58\t0.000152206860922688\t-0.00119191985006002\n+m/z = 799.67\t0.00174853153576805\t-0.0136926117080109\n+m/z = 799.75\t0.00121053975241956\t-0.00947964074305681\n+m/z = 799.83\t0.00023995237418348\t-0.00187904800165075\n+m/z = 799.92\t-1.61416057845098e-19\t-3.77958420663974e-19\n' |
| b |
| diff -r 000000000000 -r 0c1a9b68f436 test-data/pcascores_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pcascores_results1.txt Sat Feb 24 13:51:32 2018 -0500 |
| b |
| @@ -0,0 +1,10 @@ + PC1 PC2 +x = 1, y = 1 -3.10354953946922 0.882256622295169 +x = 2, y = 1 0.896503112130733 -2.98575442188371 +x = 3, y = 1 -1.57899570254884 2.26797345312228 +x = 1, y = 2 4.34938743071701 -6.43242810521544 +x = 2, y = 2 -4.25927282262866 -0.298723132409794 +x = 3, y = 2 -3.62418135901873 0.627868439327948 +x = 1, y = 3 -3.27840077885159 -1.9843074587809 +x = 2, y = 3 -1.38097137864788 4.74863282848963 +x = 3, y = 3 11.9794810383172 3.17448177505485 |
| b |
| diff -r 000000000000 -r 0c1a9b68f436 test-data/preprocessing_results1.RData |
| b |
| Binary file test-data/preprocessing_results1.RData has changed |
| b |
| diff -r 000000000000 -r 0c1a9b68f436 test-data/toplabels_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/toplabels_results1.txt Sat Feb 24 13:51:32 2018 -0500 |
| b |
| b'@@ -0,0 +1,501 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