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._.DS_Store ._CHM.R ._mda_heatmap_gen.xml ._ngchm-matrix-functional-test-data CHM.R GalaxyMapGen.jar heatmap.sh mda_heatmap_gen.xml mda_heatmap_viz.zip ngchm-matrix-functional-test-data/._.DS_Store ngchm-matrix-functional-test-data/._400x400.txt ngchm-matrix-functional-test-data/400x400-column-covariate.txt ngchm-matrix-functional-test-data/400x400-row-covariate.txt ngchm-matrix-functional-test-data/400x400.txt ngchm-matrix-functional-test-data/Galaxy400x400-noCovariates.ngchm |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ._CHM.R |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ._mda_heatmap_gen.xml |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ._ngchm-matrix-functional-test-data |
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| diff -r c71752dc05d6 -r 1b0182d3d262 CHM.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CHM.R Thu Jan 26 10:15:31 2017 -0500 |
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| @@ -0,0 +1,146 @@ +### This method generates a row and column ordering given an input matrix and ordering methods. +### +### matrixData - numeric matrix +### rowOrderMethod - Hierarchical, Original, Random +### rowDistanceMeasure - For clustering, distance measure. May be: euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation. +### rowAgglomerationMethod - For clustering, agglomeration method. May be: 'average' for Average Linkage, 'complete' for Complete Linkage, +### 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'. +### colOrderMethod +### colDistanceMeasure +### colAgglomerationMethod +### rowOrderFile - output file of order of rows +### rowDendroFile - output file of row dendrogram +### colOrderFile - output file of order of cols +### colDendroFile - output file of col dendrogram +### rowCut - For rows the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off. +### colCut - For columns the number of classifications to automatically generate based on dendrogram into a classification file. 0 for turned off. + +performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut) +{ + dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?")) + rowOrder <- createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod) + if (rowOrderMethod == "Hierarchical") { + writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile) + writeHCCut(rowOrder, rowCut, paste(rowOrderFile,".cut", sep="")) + } else { + writeOrderTSV(rowOrder, rownames(dataMatrix), rowOrderFile) + } + + colOrder <- createOrdering(dataMatrix, colOrderMethod, "col", colDistanceMeasure, colAgglomerationMethod) + if (colOrderMethod == "Hierarchical") { + writeHCDataTSVs(colOrder, colDendroFile, colOrderFile) + writeHCCut(colOrder, colCut, paste(colOrderFile,".cut", sep="")) + } else { + writeOrderTSV(colOrder, colnames(dataMatrix), colOrderFile) + } +} + +#creates output files for hclust ordering +writeHCDataTSVs<-function(uDend, outputHCDataFileName, outputHCOrderFileName) +{ + data<-cbind(uDend$merge, uDend$height, deparse.level=0) + colnames(data)<-c("A", "B", "Height") + write.table(data, file = outputHCDataFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE) + + data=matrix(,length(uDend$labels),2); + for (i in 1:length(uDend$labels)) { + data[i,1] = uDend$labels[i]; + data[i,2] = which(uDend$order==i); + } + colnames(data)<-c("Id", "Order") + write.table(data, file = outputHCOrderFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE) +} + +#creates order file for non-clustering methods +writeOrderTSV<-function(newOrder, originalOrder, outputHCOrderFileName) +{ + data=matrix(,length(originalOrder),2); + for (i in 1:length(originalOrder)) { + data[i,1] = originalOrder[i]; + data[i,2] = which(newOrder==originalOrder[i]); + } + colnames(data)<-c("Id", "Order") + write.table(data, file = outputHCOrderFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE) +} + +#creates a classification file based on user specified cut of dendrogram +writeHCCut<-function(uDend, cutNum, outputCutFileName) +{ + if (cutNum < 2) { + return() + } + print (paste("Writing cut file ", outputCutFileName)) + cut <- cutree(uDend, cutNum); + id <- names(cut); + data=matrix(,length(cut),2); + for (i in 1:length(cut)) { + data[i,1] = id[i]; + data[i,2] = sprintf("Cluster %d", cut[i]); + } + + write.table(data, file = outputCutFileName, append = FALSE, quote = FALSE, sep = "\t", row.names=FALSE, col.names = FALSE); +} + + +createOrdering<-function(matrixData, orderMethod, direction, distanceMeasure, agglomerationMethod) +{ + ordering <- NULL + + if (orderMethod == "Hierarchical") + { + + # Compute dendrogram for "Distance Metric" + distVals <- NULL + if(direction=="row") { + if (distanceMeasure == "correlation") { + geneGeneCor <- cor(t(matrixData), use="pairwise") + distVals <- as.dist((1-geneGeneCor)/2) + } else { + distVals <- dist(matrixData, method=distanceMeasure) + } + } else { #column + if (distanceMeasure == "correlation") { + geneGeneCor <- cor(matrixData, use="pairwise") + distVals <- as.dist((1-geneGeneCor)/2) + } else { + distVals <- dist(t(matrixData), method=distanceMeasure) + } + } + +# if (agglomerationMethod == "ward") { +# ordering <- hclust(distVals * distVals, method="ward.D2") +# } else { + ordering <- hclust(distVals, method=agglomerationMethod) +# } + } + else if (orderMethod == "Random") + { + if(direction=="row") { + headerList <- rownames(matrixData) + ordering <- sample(headerList, length(headerList)) + } else { + headerList <- colnames(matrixData) + ordering <- sample(headerList, length(headerList)) + } + } + else if (orderMethod == "Original") + { + if(direction=="row") { + ordering <- rownames(matrixData) + } else { + ordering <- colnames(matrixData) + } + } else { + stop("createOrdering -- failed to find ordering method") + } + return(ordering) +} +### Initialize command line arguments and call performDataOrdering + +options(warn=-1) + +args = commandArgs(TRUE) + +performDataOrdering(dataFile=args[1], rowOrderMethod=args[2], rowDistanceMeasure=args[3], rowAgglomerationMethod=args[4], colOrderMethod=args[5], colDistanceMeasure=args[6], colAgglomerationMethod=args[7],rowOrderFile=args[8], colOrderFile=args[9], rowDendroFile=args[10], colDendroFile=args[11], rowCut=args[12], colCut=args[13]) + +#suppressWarnings(performDataOrdering(dataFile=args[1], rowOrderMethod=args[2], rowDistanceMeasure=args[3], rowAgglomerationMethod=args[4], colOrderMethod=args[5], colDistanceMeasure=args[6], colAgglomerationMethod=args[7],rowOrderFile=args[8], colOrderFile=args[9], rowDendroFile=args[10], colDendroFile=args[11])) |
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| diff -r c71752dc05d6 -r 1b0182d3d262 GalaxyMapGen.jar |
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| diff -r c71752dc05d6 -r 1b0182d3d262 heatmap.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.sh Thu Jan 26 10:15:31 2017 -0500 |
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| @@ -0,0 +1,47 @@ +echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} +#create temp directory for row and col order and dendro files. +tdir=${11}/$(date +%y%m%d%M%S) +echo $tdir +mkdir $tdir +#run R to cluster matrix +output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)" +rc=$?; +if [ $rc != 0 ] +then + echo $output; + if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] + then + echo ""; + echo "Note: This error can occur when there is no variation in a row or column. Try a different distance measure or remove rows/columns without variation."; + fi + exit $rc; +fi + +#there are a variable number of triplicate parameters for classification bars +count=0 +classifications='' + +#if row cut was done, add that autogenerated classification +if [ ${12} -gt 1 ] +then + classifications="Class $tdir/ROfile.txt.cut row_categorical" +fi + +#if col cut was done, add that autogenerated classification +if [ ${13} -gt 1 ] +then + classifications="$classifications Class $tdir/COfile.txt.cut col_categorical" +fi + +#now add the user provided classification files +for i in "$@"; do + if [ $count -gt 14 ] + then + classifications=$classifications' '$i + fi + count=$((count+1)) +done +#call java program to generate NGCHM viewer files. +java -jar ${11}/GalaxyMapGen.jar "${1}" "${2}" DataLayer1 $3 linear ${14} ${15} $4 $5 $6 $tdir/ROfile.txt $tdir/RDfile.txt $7 $8 $9 $tdir/COfile.txt $tdir/CDfile.txt ${10} $classifications +#clean up tempdir +rm -rf $tdir |
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| diff -r c71752dc05d6 -r 1b0182d3d262 mda_heatmap_gen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mda_heatmap_gen.xml Thu Jan 26 10:15:31 2017 -0500 |
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| b'@@ -0,0 +1,204 @@\n+<?xml version="1.0" encoding="UTF-8" ?>\n+<tool id="mda_heatmap_gen" name="NG-CHM Generator" version="6.0.2">\n+ <description>Create Clustered Heat Maps</description>\n+<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh \'$hmname\' \'$hmdesc\' \'$inputmatrix\' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod \'$__tool_directory__\' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType\n+ #for $op in $operations\n+ ${op.class_name}\n+ ${op.repeatinput.file_name}\n+ ${op.cat}\n+ #end for\n+ \t\'$output\' \n+ </command>\n+\t<stdio>\n+ <exit_code range="1:" level="fatal" />\n+\t</stdio>\n+ <inputs>\n+ <param name="inputmatrix" type="data" label="Input Matrix" />\n+ <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>\n+ <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>\n+ <param name="summarymethod" \ttype="select" label="Data Summarization Method">\n+\t\t<option value="average">average</option>\n+\t\t<option value="sample">sample</option>\n+\t\t<option value="mode">mode</option>\n+ </param>\n+ <conditional name="d_rows">\n+\t<param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">\n+\t\t<option value="Hierarchical">Hierarchical Clustering</option>\n+\t\t<option value="Original">Original Order</option>\t \n+\t\t<option value="Random">Random</option>\t \n+\t</param>\n+ <when value="Hierarchical">\n+\t<param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation">\n+\t\t<option value="euclidean">Euclidean</option>\n+\t\t<option value="binary">Binary</option>\n+\t\t<option value="manhattan">Manhattan</option>\n+\t\t<option value="maximum">Maximum</option>\n+\t\t<option value="canberra">Canberra</option>\t \n+\t\t<option value="minkowski">Minkowski</option>\t \n+\t\t<option value="correlation">Correlation</option>\t \n+\t</param>\n+\t<param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: \'average\' for Average Linkage, \'complete\' for Complete Linkage, \'single\' for Single Linkage, \'ward\', \'mcquitty\', \'median\', or \'centroid\'.">\n+\t\t<option value="average">Average Linkage</option>\n+\t\t<option value="complete">Complete Linkage</option>\n+\t\t<option value="single">Single Linkage</option>\n+\t\t<option value="ward" selected="true">Ward</option>\n+\t\t<option value="mcquitty">Mcquitty</option>\t \n+\t\t<option value="median">Median</option>\t \n+\t\t<option value="centroid">Centroid</option>\t \n+\t</param>\n+ <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >\n+ \t\t<option value="0" selected="true" >None</option>\n+ \t\t<option value="2" >2</option>\n+ \t\t<option value="3" >3</option>\n+ \t\t<option value="4" >4</option>\n+ \t\t<option value="5" >5</option>\n+ \t\t<option value="6" >6</option>\n+ \t\t<option value="7" >7</option>\n+ \t\t<option value="8" >8</option>\n+ \t\t<option value="9" >9</option>\n+ \t\t<option value="10" >10</option>\n+ </param>\n+ </when>\n+ <when value="Original">\n+\t\t <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowDendroCut" size="0" type="text" value="0"/>\n+ </when>\n+ <when value="Random">\n+\t\t <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="rowDe'..b'+ \t\t<option value="8" >8</option>\n+ \t\t<option value="9" >9</option>\n+ \t\t<option value="10" >10</option>\n+ </param>\n+ </when>\n+ <when value="Original">\n+\t\t <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="colDendroCut" type="text" size="0" value="0"/>\n+ </when>\n+ <when value="Random">\n+\t\t <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>\n+\t\t <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>\n+\t\t <param name="colDendroCut" type="text" size="0" value="0"/>\n+ </when>\n+ </conditional>\n+ <param name="colDataType" type="select" label="Linkouts to column data type info" >\n+ <option value="labels" selected="true" >None</option>\n+ <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>\n+ <option value="bio.feature.agilent" >Agilent Id</option>\n+ <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>\n+ <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>\n+ <option value="bio.gene.entrez" >Gene Entrez Id</option>\n+ <option value="bio.gene.hugo" >Gene HUGO symbol</option>\n+ <option value="bio.go" >Gene Ontology (GO) Id</option>\n+ <option value="bio.geo.acc" >GEO Accession Id</option>\n+ <option value="bio.probe.illumina" >Illumina Probe Id</option>\n+ <option value="bio.probe.infinium" >Infinium Probe Id</option>\n+ <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>\n+ <option value="bio.mirna" >miRNA Id</option>\n+ <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>\n+ <option value="bio.pubmed" >Pubmed Id</option>\n+ <option value="bio.pubmed.search" >Pubmed Search Term</option>\n+ <option value="scholar" >Scholarly term</option>\n+ <option value="bio.gene.unigene" >Unigene CId</option>\n+ <option value="bio.protein.uniprot" >UniProt Id</option>\n+ </param> \n+ <repeat name="operations" title="Covariate Bars">\n+ <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">\n+ <sanitizer invalid_char="_">\n+ <valid initial="none">\n+ <add preset="string.letters"/>\n+ <add preset="string.digits"/>\n+ </valid>\n+ <mapping initial="none">\n+ </mapping>\n+ </sanitizer>\n+ </param>\n+ <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>\n+\t<param name="cat" type="select" label="Axis Covariate Type">\n+\t <option value="row_categorical" >row categorical</option>\n+\t <option value="row_continuous" >row continuous</option>\n+\t <option value="column_categorical" >column categorical</option>\n+\t <option value="column_continuous" >column continuous</option>\n+\t</param>\n+ </repeat> \n+ </inputs>\n+ <outputs>\n+ <data name="output" label=\'${hmname}\' format="ngchm"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="inputmatrix" value="400x400.txt" />\n+ <param name="hmname" value="testRun" />\n+ <param name="$hmdesc" value="validateTool" />\n+ <param name="summarymethod" value="average" />\n+ <param name="rowOrderMethod" value="Hierarchical" />\n+ <param name="rowDistanceMeasure" value="manhattan" />\n+ <param name="rowAgglomerationMethod" value="ward" />\n+ <param name="columnOrderMethod" value="Hierarchical" />\n+ <param name="columnDistanceMeasure" value="manhattan" />\n+ <param name="columnAgglomerationMethod" value="ward" />\n+ <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> \n+\n+ </test>\n+<!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->\n+ </tests>\n+ </tool>\n' |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/._.DS_Store |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/._400x400.txt |
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| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/400x400-column-covariate.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngchm-matrix-functional-test-data/400x400-column-covariate.txt Thu Jan 26 10:15:31 2017 -0500 |
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| b'@@ -0,0 +1,1 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No newline at end of file\n' |
| b |
| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/400x400-row-covariate.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngchm-matrix-functional-test-data/400x400-row-covariate.txt Thu Jan 26 10:15:31 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +Gene_1 aaa Gene_2 aaa Gene_3 aaa Gene_4 aaa Gene_5 aaa Gene_6 aaa Gene_7 bb Gene_8 bb Gene_9 bb Gene_10 bb Gene_11 bb Gene_12 bb Gene_13 bb Gene_14 bb Gene_15 bb Gene_16 bb Gene_17 bb Gene_18 bb Gene_19 bb Gene_20 bb Gene_21 bb Gene_22 bb Gene_23 bb Gene_24 bb Gene_25 bb Gene_26 bb Gene_27 bb Gene_28 bb Gene_29 bb Gene_30 bb Gene_31 bb Gene_32 cccc Gene_33 cccc Gene_34 cccc Gene_35 cccc Gene_36 cccc Gene_37 cccc Gene_38 cccc Gene_39 cccc Gene_40 cccc Gene_41 cccc Gene_42 cccc Gene_43 cccc Gene_44 cccc Gene_45 cccc Gene_46 cccc Gene_47 cccc Gene_48 cccc Gene_49 aaa Gene_50 aaa Gene_51 aaa Gene_52 aaa Gene_53 aaa Gene_54 aaa Gene_55 bb Gene_56 bb Gene_57 aaa Gene_58 aaa Gene_59 aaa Gene_60 aaa Gene_61 aaa Gene_62 aaa Gene_63 bb Gene_64 bb Gene_65 bb Gene_66 bb Gene_67 bb Gene_68 bb Gene_69 bb Gene_70 bb Gene_71 bb Gene_72 bb Gene_73 bb Gene_74 bb Gene_75 bb Gene_76 bb Gene_77 bb Gene_78 bb Gene_79 bb Gene_80 bb Gene_81 bb Gene_82 bb Gene_83 bb Gene_84 bb Gene_85 bb Gene_86 bb Gene_87 bb Gene_88 cccc Gene_89 cccc Gene_90 cccc Gene_91 cccc Gene_92 cccc Gene_93 cccc Gene_94 cccc Gene_95 cccc Gene_96 cccc Gene_97 cccc Gene_98 cccc Gene_99 cccc Gene_100 cccc Gene_101 cccc Gene_102 cccc Gene_103 cccc Gene_104 cccc Gene_105 aaa Gene_106 aaa Gene_107 aaa Gene_108 aaa Gene_109 aaa Gene_110 aaa Gene_111 bb Gene_112 bb Gene_113 aaa Gene_114 aaa Gene_115 aaa Gene_116 aaa Gene_117 aaa Gene_118 aaa Gene_119 bb Gene_120 bb Gene_121 bb Gene_122 bb Gene_123 bb Gene_124 bb Gene_125 bb Gene_126 bb Gene_127 bb Gene_128 bb Gene_129 bb Gene_130 bb Gene_131 bb Gene_132 bb Gene_133 bb Gene_134 bb Gene_135 bb Gene_136 bb Gene_137 bb Gene_138 bb Gene_139 bb Gene_140 bb Gene_141 bb Gene_142 bb Gene_143 bb Gene_144 cccc Gene_145 cccc Gene_146 cccc Gene_147 cccc Gene_148 cccc Gene_149 cccc Gene_150 cccc Gene_151 cccc Gene_152 cccc Gene_153 cccc Gene_154 cccc Gene_155 cccc Gene_156 cccc Gene_157 cccc Gene_158 cccc Gene_159 cccc Gene_160 cccc Gene_161 aaa Gene_162 aaa Gene_163 aaa Gene_164 aaa Gene_165 aaa Gene_166 aaa Gene_167 bb Gene_168 bb Gene_169 aaa Gene_170 aaa Gene_171 aaa Gene_172 aaa Gene_173 aaa Gene_174 aaa Gene_175 bb Gene_176 bb Gene_177 bb Gene_178 bb Gene_179 bb Gene_180 bb Gene_181 bb Gene_182 bb Gene_183 bb Gene_184 bb Gene_185 bb Gene_186 bb Gene_187 bb Gene_188 bb Gene_189 bb Gene_190 bb Gene_191 bb Gene_192 bb Gene_193 bb Gene_194 bb Gene_195 bb Gene_196 bb Gene_197 bb Gene_198 bb Gene_199 bb Gene_200 cccc Gene_201 cccc Gene_202 cccc Gene_203 cccc Gene_204 cccc Gene_205 cccc Gene_206 cccc Gene_207 cccc Gene_208 cccc Gene_209 cccc Gene_210 cccc Gene_211 cccc Gene_212 cccc Gene_213 cccc Gene_214 cccc Gene_215 cccc Gene_216 cccc Gene_217 aaa Gene_218 aaa Gene_219 aaa Gene_220 aaa Gene_221 aaa Gene_222 aaa Gene_223 bb Gene_224 bb Gene_225 aaa Gene_226 aaa Gene_227 aaa Gene_228 aaa Gene_229 aaa Gene_230 aaa Gene_231 bb Gene_232 bb Gene_233 bb Gene_234 bb Gene_235 bb Gene_236 bb Gene_237 bb Gene_238 bb Gene_239 bb Gene_240 bb Gene_241 bb Gene_242 bb Gene_243 bb Gene_244 bb Gene_245 bb Gene_246 bb Gene_247 bb Gene_248 bb Gene_249 bb Gene_250 bb Gene_251 bb Gene_252 bb Gene_253 bb Gene_254 bb Gene_255 bb Gene_256 cccc Gene_257 cccc Gene_258 cccc Gene_259 cccc Gene_260 cccc Gene_261 cccc Gene_262 cccc Gene_263 cccc Gene_264 cccc Gene_265 cccc Gene_266 cccc Gene_267 cccc Gene_268 cccc Gene_269 cccc Gene_270 cccc Gene_271 cccc Gene_272 cccc Gene_273 aaa Gene_274 aaa Gene_275 aaa Gene_276 aaa Gene_277 aaa Gene_278 aaa Gene_279 bb Gene_280 bb Gene_281 aaa Gene_282 aaa Gene_283 aaa Gene_284 aaa Gene_285 aaa Gene_286 aaa Gene_287 bb Gene_288 bb Gene_289 bb Gene_290 bb Gene_291 bb Gene_292 bb Gene_293 bb Gene_294 bb Gene_295 bb Gene_296 bb Gene_297 bb Gene_298 bb Gene_299 bb Gene_300 bb Gene_301 bb Gene_302 bb Gene_303 bb Gene_304 bb Gene_305 bb Gene_306 bb Gene_307 bb Gene_308 bb Gene_309 bb Gene_310 bb Gene_311 bb Gene_312 cccc Gene_313 cccc Gene_314 cccc Gene_315 cccc Gene_316 cccc Gene_317 cccc Gene_318 cccc Gene_319 cccc Gene_320 cccc Gene_321 cccc Gene_322 cccc Gene_323 cccc Gene_324 cccc Gene_325 cccc Gene_326 cccc Gene_327 cccc Gene_328 cccc Gene_329 aaa Gene_330 aaa Gene_331 aaa Gene_332 aaa Gene_333 aaa Gene_334 aaa Gene_335 bb Gene_336 bb Gene_337 aaa Gene_338 aaa Gene_339 aaa Gene_340 aaa Gene_341 aaa Gene_342 aaa Gene_343 bb Gene_344 bb Gene_345 bb Gene_346 bb Gene_347 bb Gene_348 bb Gene_349 bb Gene_350 bb Gene_351 bb Gene_352 bb Gene_353 bb Gene_354 bb Gene_355 bb Gene_356 bb Gene_357 bb Gene_358 bb Gene_359 bb Gene_360 bb Gene_361 bb Gene_362 bb Gene_363 bb Gene_364 bb Gene_365 bb Gene_366 bb Gene_367 bb Gene_368 cccc Gene_369 cccc Gene_370 cccc Gene_371 cccc Gene_372 cccc Gene_373 cccc Gene_374 cccc Gene_375 cccc Gene_376 cccc Gene_377 cccc Gene_378 cccc Gene_379 cccc Gene_380 cccc Gene_381 cccc Gene_382 cccc Gene_383 cccc Gene_384 cccc Gene_385 aaa Gene_386 aaa Gene_387 aaa Gene_388 aaa Gene_389 aaa Gene_390 aaa Gene_391 bb Gene_392 bb Gene_393 aaa Gene_394 aaa Gene_395 aaa Gene_396 aaa Gene_397 aaa Gene_398 aaa Gene_399 bb Gene_400 bb \ No newline at end of file |
| b |
| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/400x400.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngchm-matrix-functional-test-data/400x400.txt Thu Jan 26 10:15:31 2017 -0500 |
| b |
| b'@@ -0,0 +1,401 @@\n+\tTCGA_SAMP_1\tTCGA_SAMP_2\tTCGA_SAMP_3\tTCGA_SAMP_4\tTCGA_SAMP_5\tTCGA_SAMP_6\tTCGA_SAMP_7\tTCGA_SAMP_8\tTCGA_SAMP_9\tTCGA_SAMP_10\tTCGA_SAMP_11\tTCGA_SAMP_12\tTCGA_SAMP_13\tTCGA_SAMP_14\tTCGA_SAMP_15\tTCGA_SAMP_16\tTCGA_SAMP_17\tTCGA_SAMP_18\tTCGA_SAMP_19\tTCGA_SAMP_20\tTCGA_SAMP_21\tTCGA_SAMP_22\tTCGA_SAMP_23\tTCGA_SAMP_24\tTCGA_SAMP_25\tTCGA_SAMP_26\tTCGA_SAMP_27\tTCGA_SAMP_28\tTCGA_SAMP_29\tTCGA_SAMP_30\tTCGA_SAMP_31\tTCGA_SAMP_32\tTCGA_SAMP_33\tTCGA_SAMP_34\tTCGA_SAMP_35\tTCGA_SAMP_36\tTCGA_SAMP_37\tTCGA_SAMP_38\tTCGA_SAMP_39\tTCGA_SAMP_40\tTCGA_SAMP_41\tTCGA_SAMP_42\tTCGA_SAMP_43\tTCGA_SAMP_44\tTCGA_SAMP_45\tTCGA_SAMP_46\tTCGA_SAMP_47\tTCGA_SAMP_48\tTCGA_SAMP_49\tTCGA_SAMP_50\tTCGA_SAMP_51\tTCGA_SAMP_52\tTCGA_SAMP_53\tTCGA_SAMP_54\tTCGA_SAMP_55\tTCGA_SAMP_56\tTCGA_SAMP_57\tTCGA_SAMP_58\tTCGA_SAMP_59\tTCGA_SAMP_60\tTCGA_SAMP_61\tTCGA_SAMP_62\tTCGA_SAMP_63\tTCGA_SAMP_64\tTCGA_SAMP_65\tTCGA_SAMP_66\tTCGA_SAMP_67\tTCGA_SAMP_68\tTCGA_SAMP_69\tTCGA_SAMP_70\tTCGA_SAMP_71\tTCGA_SAMP_72\tTCGA_SAMP_73\tTCGA_SAMP_74\tTCGA_SAMP_75\tTCGA_SAMP_76\tTCGA_SAMP_77\tTCGA_SAMP_78\tTCGA_SAMP_79\tTCGA_SAMP_80\tTCGA_SAMP_81\tTCGA_SAMP_82\tTCGA_SAMP_83\tTCGA_SAMP_84\tTCGA_SAMP_85\tTCGA_SAMP_86\tTCGA_SAMP_87\tTCGA_SAMP_88\tTCGA_SAMP_89\tTCGA_SAMP_90\tTCGA_SAMP_91\tTCGA_SAMP_92\tTCGA_SAMP_93\tTCGA_SAMP_94\tTCGA_SAMP_95\tTCGA_SAMP_96\tTCGA_SAMP_97\tTCGA_SAMP_98\tTCGA_SAMP_99\tTCGA_SAMP_100\tTCGA_SAMP_101\tTCGA_SAMP_102\tTCGA_SAMP_103\tTCGA_SAMP_104\tTCGA_SAMP_105\tTCGA_SAMP_106\tTCGA_SAMP_107\tTCGA_SAMP_108\tTCGA_SAMP_109\tTCGA_SAMP_110\tTCGA_SAMP_111\tTCGA_SAMP_112\tTCGA_SAMP_113\tTCGA_SAMP_114\tTCGA_SAMP_115\tTCGA_SAMP_116\tTCGA_SAMP_117\tTCGA_SAMP_118\tTCGA_SAMP_119\tTCGA_SAMP_120\tTCGA_SAMP_121\tTCGA_SAMP_122\tTCGA_SAMP_123\tTCGA_SAMP_124\tTCGA_SAMP_125\tTCGA_SAMP_126\tTCGA_SAMP_127\tTCGA_SAMP_128\tTCGA_SAMP_129\tTCGA_SAMP_130\tTCGA_SAMP_131\tTCGA_SAMP_132\tTCGA_SAMP_133\tTCGA_SAMP_134\tTCGA_SAMP_135\tTCGA_SAMP_136\tTCGA_SAMP_137\tTCGA_SAMP_138\tTCGA_SAMP_139\tTCGA_SAMP_140\tTCGA_SAMP_141\tTCGA_SAMP_142\tTCGA_SAMP_143\tTCGA_SAMP_144\tTCGA_SAMP_145\tTCGA_SAMP_146\tTCGA_SAMP_147\tTCGA_SAMP_148\tTCGA_SAMP_149\tTCGA_SAMP_150\tTCGA_SAMP_151\tTCGA_SAMP_152\tTCGA_SAMP_153\tTCGA_SAMP_154\tTCGA_SAMP_155\tTCGA_SAMP_156\tTCGA_SAMP_157\tTCGA_SAMP_158\tTCGA_SAMP_159\tTCGA_SAMP_160\tTCGA_SAMP_161\tTCGA_SAMP_162\tTCGA_SAMP_163\tTCGA_SAMP_164\tTCGA_SAMP_165\tTCGA_SAMP_166\tTCGA_SAMP_167\tTCGA_SAMP_168\tTCGA_SAMP_169\tTCGA_SAMP_170\tTCGA_SAMP_171\tTCGA_SAMP_172\tTCGA_SAMP_173\tTCGA_SAMP_174\tTCGA_SAMP_175\tTCGA_SAMP_176\tTCGA_SAMP_177\tTCGA_SAMP_178\tTCGA_SAMP_179\tTCGA_SAMP_180\tTCGA_SAMP_181\tTCGA_SAMP_182\tTCGA_SAMP_183\tTCGA_SAMP_184\tTCGA_SAMP_185\tTCGA_SAMP_186\tTCGA_SAMP_187\tTCGA_SAMP_188\tTCGA_SAMP_189\tTCGA_SAMP_190\tTCGA_SAMP_191\tTCGA_SAMP_192\tTCGA_SAMP_193\tTCGA_SAMP_194\tTCGA_SAMP_195\tTCGA_SAMP_196\tTCGA_SAMP_197\tTCGA_SAMP_198\tTCGA_SAMP_199\tTCGA_SAMP_200\tTCGA_SAMP_201\tTCGA_SAMP_202\tTCGA_SAMP_203\tTCGA_SAMP_204\tTCGA_SAMP_205\tTCGA_SAMP_206\tTCGA_SAMP_207\tTCGA_SAMP_208\tTCGA_SAMP_209\tTCGA_SAMP_210\tTCGA_SAMP_211\tTCGA_SAMP_212\tTCGA_SAMP_213\tTCGA_SAMP_214\tTCGA_SAMP_215\tTCGA_SAMP_216\tTCGA_SAMP_217\tTCGA_SAMP_218\tTCGA_SAMP_219\tTCGA_SAMP_220\tTCGA_SAMP_221\tTCGA_SAMP_222\tTCGA_SAMP_223\tTCGA_SAMP_224\tTCGA_SAMP_225\tTCGA_SAMP_226\tTCGA_SAMP_227\tTCGA_SAMP_228\tTCGA_SAMP_229\tTCGA_SAMP_230\tTCGA_SAMP_231\tTCGA_SAMP_232\tTCGA_SAMP_233\tTCGA_SAMP_234\tTCGA_SAMP_235\tTCGA_SAMP_236\tTCGA_SAMP_237\tTCGA_SAMP_238\tTCGA_SAMP_239\tTCGA_SAMP_240\tTCGA_SAMP_241\tTCGA_SAMP_242\tTCGA_SAMP_243\tTCGA_SAMP_244\tTCGA_SAMP_245\tTCGA_SAMP_246\tTCGA_SAMP_247\tTCGA_SAMP_248\tTCGA_SAMP_249\tTCGA_SAMP_250\tTCGA_SAMP_251\tTCGA_SAMP_252\tTCGA_SAMP_253\tTCGA_SAMP_254\tTCGA_SAMP_255\tTCGA_SAMP_256\tTCGA_SAMP_257\tTCGA_SAMP_258\tTCGA_SAMP_259\tTCGA_SAMP_260\tTCGA_SAMP_261\tTCGA_SAMP_262\tTCGA_SAMP_263\tTCGA_SAMP_264\tTCGA_SAMP_265\tTCGA_SAMP_266\tTCGA_SAMP_267\tTCGA_SAMP_268\tTCGA_SAMP_269\tTCGA_SAMP_270\tTCGA_SAMP_271\tTCGA_SAMP_272\tTCGA_SAMP_273\tTCGA_SAMP_274\tTCGA_SAMP_275\tTCGA_SAMP_276\tTCGA_SAMP_277\tTCGA_SAMP_278\tTCGA_SAMP_279\tTCGA_SAMP_280\tTCGA_SAMP_281\tTCGA_SAMP_282\tTCGA_SAMP_283\tTCGA_SAMP_284\tTCGA_SAMP_285\tTCGA_SAMP_286\tTCGA_SAMP_287\tTCGA_SAMP_288\tTCGA_SAMP_289\tTCGA_SAMP_290\tTCGA_SAMP_291\tTCGA_SAMP_292'..b'-0.1234\t-0.5552\t-1.0011\t-0.7683\t-0.9426\t0.4153\t-0.9074\t-0.8332\t-0.7285\t-0.7919\t-0.7821\t-0.1604\t-0.9555\t-0.5453\t-0.5558\t-0.4777\t0.9927\t-0.5413\t-0.4734\t-0.4588\t-0.5805\t-1.0253\t-0.7693\t-0.4296\t-0.6796\t0.8262\t-0.7745\t-0.6376\t-0.0074\t0.3159\t-0.9130\t-0.9774\t0.6942\t-0.5006\t-0.8757\t0.5845\t0.7145\t0.8540\t0.9361\t0.8116\t0.2409\t-0.5179\t0.8032\t1.1316\t1.0940\t0.6173\t1.0097\t0.7659\t1.1171\t0.0157\t0.6325\t1.1164\t0.4553\t0.9517\t1.0558\t0.6920\t0.5512\t-0.0023\t0.6649\t0.1056\t0.0373\t0.3099\t-0.4889\t0.2225\t0.1384\t0.1885\t0.2696\t-0.3968\t0.0435\t-0.1625\t0.3381\t-0.5490\t-0.8873\t-0.1601\t-0.0382\t-0.1281\t0.5346\t0.1330\t-0.0225\t-0.0469\t0.3917\t-0.2018\t0.0124\t0.0971\t0.0586\t-0.2148\t-0.0725\t0.2933\t0.2434\t-0.1930\t-0.2130\t-0.0815\t-0.1020\t0.1226\t-0.8454\t0.2793\t0.0076\t-0.0491\t0.4567\t-0.5813\t-0.1195\t-0.0545\t0.4301\t0.6602\t0.0026\t-0.0107\t0.0924\t0.2801\t0.0994\t0.1995\t-0.5433\t-0.1273\t-0.2183\t0.3139\t0.7543\n+Gene_400\t-0.4675\t-0.5625\t-0.9426\t-0.9125\t-0.7059\t-1.0095\t-0.5360\t0.5494\t-0.8530\t-0.6565\t-0.5113\t-0.7029\t-0.9266\t-0.5604\t-0.6257\t-0.5704\t-0.7289\t-0.8479\t0.2874\t-0.5555\t-0.7253\t0.7134\t-0.8393\t-0.7263\t-0.1907\t-0.9337\t-0.9875\t-0.9372\t-0.7513\t-0.5924\t-0.6478\t-1.0565\t-0.4282\t-1.0247\t-0.7741\t-0.7328\t-0.6240\t-0.7278\t-0.1866\t-0.7209\t-0.5869\t-0.9104\t-0.8722\t0.7306\t-0.8916\t-0.7944\t-0.7026\t0.3330\t-0.8422\t-0.8180\t-1.0085\t-0.8501\t-0.7878\t-0.0265\t-0.8514\t-0.5027\t-0.6785\t-0.7414\t-1.0339\t0.9769\t-0.8676\t-0.6131\t-0.5971\t-1.0292\t-0.7050\t-0.9822\t-0.6119\t0.8307\t0.4432\t-0.6735\t-0.7362\t0.9352\t0.3047\t-0.6156\t-0.8046\t-0.8011\t-0.9673\t-0.0873\t-0.5907\t-0.7913\t-0.6618\t-0.7793\t-0.6049\t-0.5591\t-1.0178\t-0.5226\t-0.5416\t-0.5813\t-0.8697\t0.1654\t-1.0279\t0.6686\t-0.9866\t-0.7457\t-0.6320\t-0.5601\t-0.5332\t-0.5421\t-0.2444\t-0.9276\t-0.9135\t-0.8742\t-0.9947\t-0.9066\t-0.5072\t-0.7124\t-0.6779\t-0.7269\t-0.7067\t-1.0756\t-0.7878\t-0.9654\t-0.7497\t0.8585\t-0.8088\t-0.2993\t-0.4758\t-0.6342\t-0.9970\t-0.9072\t-0.8251\t-0.5799\t-0.8863\t-0.6786\t0.1716\t-0.7152\t-0.3949\t-0.7811\t-0.7618\t-0.5131\t-0.9968\t-0.5984\t-0.7348\t-0.6830\t0.6360\t0.4276\t-0.6148\t-0.5662\t-0.4814\t-0.7204\t-1.0230\t-0.6352\t-0.8532\t-0.9810\t-1.0715\t0.5990\t-0.7936\t-0.5936\t-0.7362\t-0.8250\t-0.6988\t-0.9429\t-0.7175\t0.2144\t-0.8203\t-0.7717\t-0.6864\t0.8223\t-0.8283\t0.9115\t-0.7985\t-0.6492\t-0.8979\t-0.9065\t-0.0489\t-1.0277\t-0.3150\t-0.0747\t-0.9950\t-0.3324\t-0.0221\t0.1903\t-0.1714\t0.9333\t-0.4070\t-0.1338\t0.1442\t-0.4161\t-0.2932\t-0.5282\t-0.5717\t-0.4622\t0.8190\t-0.3340\t-0.5111\t-0.0428\t-0.2564\t-0.2569\t-0.1697\t0.4051\t-0.6920\t-0.3264\t-0.0712\t-0.2308\t-0.1695\t-0.0590\t-0.3065\t-0.1910\t-0.1837\t-0.1376\t-0.2802\t0.4537\t-0.5248\t-0.2884\t-0.3138\t-0.3883\t-0.0174\t-0.0968\t0.1407\t-0.2415\t-0.4150\t0.2691\t-0.2863\t-0.0553\t-0.1940\t-0.3862\t-0.5521\t0.3513\t0.5377\t-0.0957\t-0.1367\t-0.0404\t-0.6388\t0.7555\t0.6765\t-0.2095\t0.1232\t0.9740\t0.0258\t-0.2023\t-0.2714\t-0.2547\t-0.0517\t-0.3214\t0.6261\t-0.0485\t-0.0965\t-0.1772\t-0.0664\t-0.2283\t-0.0235\t-0.3385\t-0.5397\t0.9498\t-0.2252\t-0.4920\t0.3937\t-0.9364\t-0.0602\t0.1564\t-0.7009\t0.4962\t0.5710\t-0.2458\t-0.0143\t-0.4776\t-0.2535\t-0.1612\t-0.2521\t-0.4946\t-0.3643\t-0.0460\t0.6374\t-0.5389\t-0.6337\t-0.1551\t-0.1683\t-0.2280\t-0.5649\t0.1563\t-0.3811\t-0.5550\t-0.3368\t-0.3596\t-0.9880\t-0.8343\t-0.3819\t-0.2793\t0.6773\t0.0126\t-0.4956\t-0.5080\t-0.4040\t-0.0193\t-0.3502\t-0.5371\t-0.1358\t-0.2151\t-0.6968\t-0.0244\t-0.4420\t-0.7311\t-0.4241\t-0.3395\t-0.1330\t-0.4521\t-0.2395\t-0.1335\t-0.1596\t-0.4195\t-0.7585\t-0.3474\t0.2321\t-0.2345\t-0.3285\t0.8975\t-0.1729\t-0.5696\t-0.4128\t-0.3681\t-0.1093\t-0.0937\t0.0969\t-0.7263\t-0.9508\t-0.2285\t-0.1364\t-0.2778\t-0.2074\t-0.1128\t-0.0071\t0.3693\t0.2008\t-0.0301\t0.8537\t-0.0354\t-0.3364\t-0.6988\t-0.4083\t-0.4346\t-0.5064\t-0.3832\t-0.1229\t0.4540\t-0.5451\t-0.2981\t0.0137\t-0.9264\t0.3926\t0.7172\t0.1079\t-0.9814\t-0.6913\t-0.2629\t0.5726\t-0.9126\t-0.1970\t0.0353\t0.0183\t0.0080\t0.1573\t-0.1910\t0.1862\t-0.1535\t-0.0711\t0.0457\t-0.0962\t-0.9497\t-0.2888\t0.0767\t-0.2824\t0.0747\t0.1759\t-0.3013\t0.1017\t-0.1491\t-0.3433\t-0.3226\t-0.1821\t-0.0231\t0.1140\t-0.9329\t-0.7741\t0.9107\t-0.8045\t-0.5862\t-0.8495\t0.7974\t-0.9572\t-0.4193\t-0.9811\t0.4838\t-0.5628\t-0.4886\t0.4722\t-0.6954\t-0.4979\t-0.7257\t-0.8920\t-0.3473\t0.9870\t-0.5745\t-0.8121\t-0.5114\t-1.0267\t-0.2803\t-0.5134\t-0.8283\t0.4809\t-0.5844\n' |
| b |
| diff -r c71752dc05d6 -r 1b0182d3d262 ngchm-matrix-functional-test-data/Galaxy400x400-noCovariates.ngchm |
| b |
| Binary file ngchm-matrix-functional-test-data/Galaxy400x400-noCovariates.ngchm has changed |