# HG changeset patch # User insilico-bob # Date 1561045013 14400 # Node ID 1f13d304ddbd818e578d24c2f3badc7a6d82c787 # Parent 15c71ed09efa1c2c7680cace56dcba1132d30bc8 Uploaded diff -r 15c71ed09efa -r 1f13d304ddbd CHM_Advanced.R --- a/CHM_Advanced.R Thu Nov 08 14:59:57 2018 -0500 +++ b/CHM_Advanced.R Thu Jun 20 11:36:53 2019 -0400 @@ -17,7 +17,7 @@ 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","-","?")) + dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", check.names = FALSE, 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) diff -r 15c71ed09efa -r 1f13d304ddbd GalaxyMapGen.jar Binary file GalaxyMapGen.jar has changed diff -r 15c71ed09efa -r 1f13d304ddbd heatmap_advanced.sh --- a/heatmap_advanced.sh Thu Nov 08 14:59:57 2018 -0500 +++ b/heatmap_advanced.sh Thu Jun 20 11:36:53 2019 -0400 @@ -1,39 +1,355 @@ -#echo "1: " $1 -#echo "2: " $2 -#echo "3: " $3 -#echo "4: " $4 -#echo "5: " $5 -#echo "6: " $6 -#echo "7: " $7 -#echo "8: " $8 -#echo "9: " $9 -#echo "10: " ${10} -#echo "11: " ${11} -#echo "12: " ${12} -#echo "13: " ${13} -#echo "14: " ${14} -#echo "15: " ${15} -#echo "16: " ${16} -#echo "17: " ${17} -#echo "18: " ${18} -#echo "19: " ${19} -#echo "20: " ${20} -#echo "21: " ${21} -#echo "22: " ${22} -#echo "23: " ${23} -#echo "23: " ${24} -#echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23} +#echo "1: " $1 " 2: " $2 " 3: " $3 " 4: " $4 " 5: " $5 " 6: " $6 " 7: " $7 " 8: " $8 " 9: " $9 " 10: " ${10} +#echo "11: " ${11} " 12: " ${12} 13: " ${13} 14: " ${14} " 15: " ${15} " 16: " ${16} " 17: " ${17} " 18: " ${18} " 19: " ${19} " 20: " ${20} +#echo "21: "${21}" 22: "${22}" 23: "${23}" 24: "${24}" 25: "${25}" 26: "${26}" 27: "${27}" 28: "${28}" 29: "${29}" 30: "${30} -#get tool data and tool install directories -tooldir=$(cut -d';' -f1 <<< ${12}) -tooldata=$(cut -d';' -f2 <<< ${12}) +#Count total number of parameters, dataLayer parameters, and classification parameters +parmSize=0 +classSize=0 +dataLayerSize=0 +attribSize=0 +for i in "$@"; do + currParm=$(cut -d'|' -f1 <<< $i) + parmSize=$((parmSize+1)) + if [ $currParm = "classification" ] + then + classSize=$((classSize+1)) + fi + if [ $currParm = "matrix_files" ] + then + dataLayerSize=$((dataLayerSize+1)) + fi + if [ $currParm = "attribute" ] + then + attribSize=$((attribSize+1)) + fi +done +if [ $dataLayerSize -lt 1 ] +then + noDataLayer="ERROR: No Heat Map Matrices provided. Please add at least one Heat Map Matrix to your request and try again." + echo $noDataLayer + exit $noDataLayer +fi + +#Get tool data and tool install directories +tooldir=$1 +tooldata=$2 #create temp directory for row and col order and dendro files. tdir=$tooldata/$(date +%y%m%d%M%S) -echo $tdir mkdir $tdir +#echo "tdir: "$tdir + +#Extract parameters for row and column order and dendro files +rowOrderFile=$tdir/ROfile.txt +rowDendroFile=$tdir/RDfile.txt +colOrderFile=$tdir/COfile.txt +colDendroFile=$tdir/CDfile.txt +rowOrderJson='"order_file": "'$rowOrderFile'",' +rowDendroJson='"dendro_file": "'$rowDendroFile'",' +colOrderJson='"order_file": "'$colOrderFile'",' +colDendroJson='"dendro_file": "'$colDendroFile'",' + +#BEGIN: Construct JSON for all non-repeating parameters +parmJson='{' +rowConfigJson='"row_configuration": {' +colConfigJson='"col_configuration": {' + +ctr=0 +for i in "$@"; do + if [ $ctr -gt 1 ] + then + currParm=$(cut -d'|' -f1 <<< $i) + if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ] && [ $currParm != "attribute" ] + then + #Parse pipe-delimited parameter parameter + parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",' + fi + if [ $currParm = "row_configuration" ] + then + rowOrder=$(cut -d'|' -f3 <<< $i) + rowDistance=$(cut -d'|' -f5 <<< $i) + rowAgglomeration=$(cut -d'|' -f7 <<< $i) + rowCuts=$(cut -d'|' -f9 <<< $i) + rowLabels=$(cut -d'|' -f11 <<< $i) + rowDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"],' + rowCutType=$(cut -d'|' -f16 <<< $i) + rowTopItemsJson='' + rowTopItems=$(cut -d'|' -f13 <<< $i) + if [ $rowTopItems != "None" ] && [ $rowTopItems != "" ] + then + rowTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": [' + rowTopItems=${rowTopItems//,/'","'} + rowTopItemsJson=$rowTopItemsJson'"'$rowTopItems'"],' + fi + rowCutsJson='' + if [ $rowCutType != "none" ] + then + cutValues=$(cut -d'|' -f15 <<< $i) + if [ $cutValues != "None" ] && [ $cutValues != "0" ] + then + if [ $rowCutType = "treecuts" ] + then + rowCutsJson=$rowCutsJson'"tree_cuts": "'$cutValues'",' + rowCutsJson=$rowCutsJson'"cut_width": "5",' + fi + if [ $rowCutType = "positional" ] + then + rowCutErrorVal=0 + [[ $cutValues != ?(-)+([0-9,]) ]] && rowCutErrorVal=$((rowCutErrorVal+1)) + if [ $rowCutErrorVal -gt 0 ] + then + echo "GALAXY PARAMETER WARNING: Non-numeric values found for Row Fixed Gap Locations. Ignoring parameter value: "$cutValues + else + rowCutsJson=$rowCutsJson'"cut_locations": ['$cutValues'],' + rowCutsJson=$rowCutsJson'"cut_width": "5",' + fi + fi + fi + fi + rowConfigJson=$rowConfigJson$rowDataTypeJson$rowCutsJson$rowTopItemsJson + if [ $rowOrder = 'Hierarchical' ] + then + rowConfigJson=$rowConfigJson$rowOrderJson$rowDendroJson + fi + rowConfigJson=$rowConfigJson' "'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},' + fi + if [ $currParm = "col_configuration" ] + then + colOrder=$(cut -d'|' -f3 <<< $i) + colDistance=$(cut -d'|' -f5 <<< $i) + colAgglomeration=$(cut -d'|' -f7 <<< $i) + colCuts=$(cut -d'|' -f9 <<< $i) + colLabels=$(cut -d'|' -f11 <<< $i) + colDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"],' + colCutType=$(cut -d'|' -f16 <<< $i) + colTopItemsJson='' + colTopItems=$(cut -d'|' -f13 <<< $i) + if [ $colTopItems != "None" ] && [ $colTopItems != "" ] + then + colTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": [' + colTopItems=${colTopItems//,/'","'} + colTopItemsJson=$colTopItemsJson'"'$colTopItems'"],' + fi + colCutsJson='' + if [ $colCutType != "none" ] + then + cutValues=$(cut -d'|' -f15 <<< $i) + if [ $cutValues != "None" ] && [ $cutValues != "0" ] + then + if [ $colCutType = "treecuts" ] + then + colCutsJson=$colCutsJson'"tree_cuts": "'$cutValues'",' + colCutsJson=$colCutsJson'"cut_width": "5",' + fi + if [ $colCutType = "positional" ] + then + colCutErrorVal=0 + [[ $cutValues != ?(-)+([0-9,]) ]] && colCutErrorVal=$((colCutErrorVal+1)) + if [ $colCutErrorVal -gt 0 ] + then + echo "GALAXY PARAMETER WARNING: Non-numeric values found for Column Fixed Gap Locations. Ignoring parameter value: "$cutValues + else + colCutsJson=$colCutsJson'"cut_locations": ['$cutValues'],' + colCutsJson=$colCutsJson'"cut_width": "5",' + fi + fi + fi + fi + colConfigJson=$colConfigJson$colDataTypeJson$colCutsJson$colTopItemsJson + if [ $colOrder = 'Hierarchical' ] + then + colConfigJson=$colConfigJson$colOrderJson$colDendroJson + fi + colConfigJson=$colConfigJson' "'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},' + fi + fi + ctr=$((ctr+1)) +done + +#END: Construct JSON for all non-repeating parameters +#echo "rowOrder: "$rowOrder +#echo "rowDistance: "$rowDistance +#echo "rowAgglomeration: "$rowAgglomeration +#echo "rowCuts: "$rowCuts +#echo "rowLabels: "$rowLabels +#echo "ROW CONFIG JSON: "$rowConfigJson +#echo "colOrder: "$colOrder +#echo "colDistance: "$colDistance +#echo "colAgglomeration: "$colAgglomeration +#echo "colCuts: "$colCuts +#echo "colLabels: "$colLabels +#echo "COL CONFIG JSON: "$colConfigJson + +#BEGIN: Construct JSON for data layers +matrixJson='"matrix_files": [ ' +inputMatrix='' +dataLayerIter=0 +dataLayerNames='' +for i in "$@"; do + currParm=$(cut -d'|' -f1 <<< $i) + if [ $currParm = "matrix_files" ] + then + if [ $dataLayerIter -lt 1 ] + then + inputMatrix=$(cut -d'|' -f3 <<< $i) + fi + currMatrixName=$(cut -d'|' -f5 <<< $i) + dataLayerIter=$((dataLayerIter+1)) + if [[ $dataLayerNames =~ $currMatrixName ]] + then + currMatrixName=$currMatrixName$dataLayerIter + fi + dataLayerNames=$dataLayerNames$currMatrixName + colorPref=$(cut -d'|' -f16 <<< $i) + colorMapJson='' + if [ $colorPref = "defined" ] + then + #validations to place leading zero on first breakpoint (if necessary) + b1=$(cut -d'|' -f20 <<< $i) + b1first=$(cut -d'.' -f1 <<< $b1) + if [ $b1first = "-" ] + then + b1="-0."$(cut -d'.' -f2 <<< $b1) + fi + if [ "$b1first" = "" ] + then + b1="0"$b1 + fi + #validations to place leading zero on second breakpoint (if necessary) + b2=$(cut -d'|' -f21 <<< $i) + b2first=$(cut -d'.' -f1 <<< $b2) + if [ $b2first = "-" ] + then + b2="-0."$(cut -d'.' -f2 <<< $b2) + fi + if [ "$b2first" = "" ] + then + b2="0"$b2 + fi + #validations to place leading zero on third breakpoint (if necessary) + b3=$(cut -d'|' -f22 <<< $i) + b3first=$(cut -d'.' -f1 <<< $b3) + if [ $b3first = "-" ] + then + b3="-0."$(cut -d'.' -f2 <<< $b3) + fi + if [ "$b3first" = "" ] + then + b3="0"$b3 + fi + #validation to ensure that all entered breakpoints are numeric values + regExp='^[+-]?([0-9]+\.?|[0-9]*\.[0-9]+)$' + if [[ $b1 =~ $regExp ]] && [[ $b2 =~ $regExp ]] && [[ $b3 =~ $regExp ]] + then + colorMapJson=$colorMapJson'"color_map": {"colors": ["'$(cut -d'|' -f17 <<< $i)'","'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'"],' + colorMapJson=$colorMapJson'"thresholds": ['$b1','$b2','$b3'],' + colorMapJson=$colorMapJson'"missing":"'$(cut -d'|' -f23 <<< $i)'"},' + else + echo "GALAXY PARAMETER WARNING: Not all user-defined breakpoints are numbers. Defined breakpoints and colors will be ignored." + fi + fi + #Parse pipe-delimited parameter parameter + matrixJson=$matrixJson' {'$colorMapJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$currMatrixName'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f10 <<< $i)'":"'$(cut -d'|' -f11 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"}' + if [ $dataLayerIter -lt $dataLayerSize ] + then + matrixJson=$matrixJson',' + fi + fi +done +matrixJson=$matrixJson"]," +#END: Construct JSON for data layers +#echo "DATA LAYER JSON: "$matrixJson +#echo "INPUT MATRIX: "$inputMatrix + +#BEGIN: Construct JSON for attributes +attribJson='"chm_attributes": [ ' +attribIter=0 +for i in "$@"; do + currParm=$(cut -d'|' -f1 <<< $i) + if [ $currParm = "attribute" ] + then + attribIter=$((attribIter+1)) + attribParam=$(cut -d'|' -f2 <<< $i) + #Parse pipe-delimited 2-part data layer parameter + attribJson=$attribJson' {"'$(cut -d':' -f1 <<< $attribParam)'":"'$(cut -d':' -f2 <<< $attribParam)'"}' + if [ $attribIter -lt $attribSize ] + then + attribJson=$attribJson',' + fi + fi +done +attribJson=$attribJson'],' +#END: Construct JSON for attributes +#echo "ATTRIB JSON: "$attribJson + +#BEGIN: Construct JSON for classification files +classJson='"classification_files": [ ' +colCutClass='' +rowCutClass='' +if [ $rowCuts -gt 1 ] +then + rowCutClass='{"name": "Class", "path": "'$tdir'/ROfile.txt.cut","position": "row", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}' +fi + +if [ $colCuts -gt 1 ] +then + if [ $rowCuts -gt 1 ] + then + rowCutClass=$rowCutClass',' + fi + colCutClass='{"name": "Class", "path": "'$tdir'/COfile.txt.cut","position": "column", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}' + if [ $classSize -gt 0 ] + then + colCutClass=$colCutClass',' + fi +else + if [ $rowCuts -gt 1 ] && [ $classSize -gt 0 ] + then + rowCutClass=$rowCutClass',' + fi +fi + +classJson=$classJson$rowCutClass$colCutClass +classIter=0 +for i in "$@"; do + currParm=$(cut -d'|' -f1 <<< $i) + if [ $currParm = "classification" ] + then + classIter=$((classIter+1)) + className=$(cut -d'|' -f3 <<< $i) + #Parse pipe-delimited 3-part classification bar parameter + classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"' + classCat=$(cut -d'|' -f7 <<< $i) + classColorType=$(cut -d'_' -f2 <<< $classCat) + classJson=$classJson',' + classHeight=$(cut -d'|' -f11 <<< $i) + heightErrorVal=0 + [[ $classHeight != ?(-)+([0-9]) ]] && heightErrorVal=$((heightErrorVal+1)) + if [ $heightErrorVal -gt 0 ] + then + echo 'GALAXY PARAMETER WARNING: Non-numeric values found for covariate bar ('$className') height. Height value ignored and default of 15 used: '$classHeight + else + classJson=$classJson'"height": "'$classHeight'",' + fi + classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}' + if [ $classIter -lt $classSize ] + then + classJson=$classJson',' + fi + fi +done +classJson=$classJson']' +#END: Construct JSON for classification files +#echo "CLASSIFICATION JSON: "$classJson + +#Complete construction of Parameter JSON file by adding all JSON sections created above +parmJson=$parmJson$rowConfigJson$colConfigJson$attribJson$matrixJson$classJson +parmJson=$parmJson'}' +#echo "COMPLETED PARAMETER JSON: "$parmJson + #run R to cluster matrix -output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)" +output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)" +# Check for errors from R step, log them if found, and exit script rc=$?; if [ $rc != 0 ] then @@ -41,40 +357,13 @@ if [ `echo "$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."; - echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; + echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry."; + echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix. 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 [ ${13} -gt 1 ] -then - classifications="Class $tdir/ROfile.txt.cut row_categorical color_plot" -fi - -#if col cut was done, add that autogenerated classification -if [ ${14} -gt 1 ] -then - classifications="$classifications Class $tdir/COfile.txt.cut col_categorical color_plot" -fi - -#now add the user provided classification files -for i in "$@"; do - if [ $count -gt 20 ] - then -# echo "class entry: " $i - classifications=$classifications' '$i - fi - count=$((count+1)) -done -#echo "classifications: " $classifications - -#call java program to generate NGCHM viewer files. -java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt "${17}" "${19}" $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt "${18}" "${20}" ${11} "${21}" $classifications +#Call java program to generate NGCHM viewer files. +java -jar $tooldir/GalaxyMapGen.jar "$parmJson" #clean up tempdir rm -rf $tdir diff -r 15c71ed09efa -r 1f13d304ddbd mda_advanced_heatmap_gen.xml --- a/mda_advanced_heatmap_gen.xml Thu Nov 08 14:59:57 2018 -0500 +++ b/mda_advanced_heatmap_gen.xml Thu Jun 20 11:36:53 2019 -0400 @@ -2,30 +2,76 @@ r-base - openjdk + openjdk Create Clustered Heat Maps with Advanced Options -$__tool_directory__/heatmap_advanced.sh 'advanced' 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' - - " +$__tool_directory__/heatmap_advanced.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth" + "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}" + "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}" #for $attr in $hm_attribute - '${attr.attrbute_key}':'${attr.attrbute_value}'; + 'attribute|${attr.attrbute_key}':'${attr.attrbute_value}' #end for - " - + #for $mx in $matrices + 'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}' + #end for #for $op in $operations - '${op.class_name}' - '${op.repeatinput.file_name}' - '${op.cattype.cat}' - '${op.cattype.bartype}' - #end for - '$output' + 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}' + #end for + 'output_location|$output' - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -44,10 +90,16 @@ - - - - + + + + + + + + + + @@ -58,12 +110,12 @@ - + - + - + @@ -71,9 +123,22 @@ - - + + + + + + + + + + + + + + @@ -97,16 +162,16 @@ - - - - - - - - - - + + + + + + + + + + @@ -180,12 +245,12 @@ - + - + - + @@ -193,10 +258,23 @@ - - + - + + + + + + + + + + + + + + @@ -219,16 +297,16 @@ - - - - - - - - - - + + + + + + + + + + @@ -305,32 +383,77 @@ + - + - + - - - - - + + + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + - - + + + + + + + + + + diff -r 15c71ed09efa -r 1f13d304ddbd mda_heatmap_viz.zip Binary file mda_heatmap_viz.zip has changed