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1 #!/usr/bin/Rscript
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2
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3 ## --------------------
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4 ## prints all arguments as msg
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5 ## --------------------
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6 catMsg <- function( msg=c() ){
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7 cat( MAIN_NAME, paste( msg, collapse="" ), "\n", sep='')
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8 }
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9 ## --------------------
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28
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10 ## return the location of this script
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2
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11 ## --------------------
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12 getScriptPath <- function(){
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13 cmd.args <- commandArgs()
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14 m <- regexpr("(?<=^--file=).+", cmd.args, perl=TRUE)
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15 script.dir <- dirname(regmatches(cmd.args, m))
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42
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16 if( length(script.dir) == 0 ) stop("[ERR] Can't determine script dir: please call the script with Rscript\n")
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17 if( length(script.dir) > 1 ) stop("[ERR] Can't determine script dir: more than one '--file' argument detected\n")
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2
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18 return(script.dir)
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19 }
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20 ## --------------------
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28
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21 ## Some html creation functions
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2
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22 ## --------------------
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23 htmlTableRow <- function( string_array=c() ){
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24 td_cells <- ''
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25 for ( i in string_array ){
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26 td_cells <- paste( td_cells, '<td>', i, '</td>', sep='' )
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27 }
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28 return( paste( "<tr>", td_cells, "</tr>") )
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29 }
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30 htmlLink <- function( path, desc="LINK" ){
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31 return( paste( '<a href="', path, '">', desc, "</a>", sep='') )
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32 }
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33 ## --------------------
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28
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34 ## constructs a list with input bam file info
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2
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35 ## --------------------
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36 makeBamFileList <- function( paths, names ){
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37 tmp <- list()
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38 l1 <- length(paths)
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39 l2 <- length(names)
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42
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40 if ( l1 != l2 ) stop( "Unequal amount of bam-paths (", l1, ") and -names (", l2, ") in makeBamFileList!!!\n" )
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2
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41 for ( i in 1:length(paths) ){
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42 path <- paths[i]
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43 name <- names[i]
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44 file <- basename(path)
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45
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46 tmp[[ file ]] <- name
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47 tmp[[ 'all_paths' ]] <- c( tmp[[ 'all_paths' ]], path )
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48 tmp[[ 'all_files' ]] <- c( tmp[[ 'all_files' ]], file )
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49 tmp[[ 'all_names' ]] <- c( tmp[[ 'all_names' ]], name )
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50 }
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51 return( tmp )
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52 }
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53
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54 ## --------------------
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28
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55 ## copied code for extracting the regions by segment call status
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2
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56 ## --------------------
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59
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57 fuseRegions <- function( cgh, onlyCalled=T ) {
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58 if ( ncol(cgh) > 1 ) stop('Please specify which sample...')
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2
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59
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59
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60 data <- data.frame( cgh@featureData@data[,1:3], calls(cgh), copynumber(cgh), segmented(cgh), check.names=FALSE, stringsAsFactors=FALSE)
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61 colnames( data ) <- c( "chr", "start", "end", "call", "log2", "segmentval" )
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62
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63 fused.data <- data.frame()
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64 curr.bin <- 1
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59
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65 for ( chr in unique( data$chr ) ) {
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66
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59
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67 chr.data <- data[ data$chr == chr, ]
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68 prev.bin <- curr.bin
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69 prev.call <- chr.data[ 1, 'call' ]
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70 prev.log2 <- chr.data[ 1, 'log2' ]
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71 prev.segm <- chr.data[ 1, 'segmentval' ]
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72 start <- chr.data[ 1, 'start' ]
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2
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73
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74 if ( nrow(chr.data) > 1) {
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75 for ( i in 2:nrow(chr.data) ) {
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76
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59
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77 curr.bin <- curr.bin + 1
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78 curr.call <- chr.data[ i, 'call']
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79 curr.segm <- chr.data[ i, 'segmentval']
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80
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81 if ( curr.segm != prev.segm ) {
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82
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83 fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], call=prev.call, segmentval=round(prev.segm, digits=DECIMALS) ) )
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84 if ( prev.call != 0 ){
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42
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85 catMsg( c(" ...found called/segmented region (", chr, ':', start, ' call=', prev.call, ' segment=', prev.segm, ")" ) )
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2
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86 }
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87 prev.call <- curr.call
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88 prev.segm <- curr.segm
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89 prev.bin <- curr.bin
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90 start <- chr.data[ i, 'start']
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2
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91 }
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92 }
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93 fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], call=prev.call, segmentval=round(prev.segm, digits=DECIMALS) ) )
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59
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94 }else{
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95 fused.data <- rbind( fused.data, data.frame( chr=chr, start=start, end=chr.data[ i-1, 'end'], call=prev.call, segmentval=round(prev.segm, digits=DECIMALS) ) )
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96 }
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97 }
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59
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98 ## if requested remove the regions with call status 0 (= normal)
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99 if ( onlyCalled == T ){
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100 fused.data <- fused.data[ fused.data$call != 0, ]
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101 }
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102 fused.data
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103 }
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104
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105 ## DESC: takes the output of fuse.regions and outputs a txt file per sample
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106 outputRegionsFromList <- function ( regionsList, outputBasename, outputDir="./" ){
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107 if ( missing(regionsList) ) stop( 'Please provide regionsList...' )
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108 if ( missing(outputBasename) ) stop( 'Please provide outputBasename...' )
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109 if ( !is.list(regionsList) ) stop( 'Input not a list...?' )
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110 if ( length(regionsList) < 1 ) stop( 'List seems empty...?' )
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42
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111 if ( file.exists( outputDir ) ) catMsg( c(" Using dir ", outputDir, " for output") )
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112 else dir.create( outputDir )
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113 outFiles <- list()
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114
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115 ## have to set R output options otherwise scientific method is used at some point
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116 options( "scipen"=100 )
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117
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118 sampleCount <- length( regionsList )
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119 sampleNames <- names( regionsList )
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120 bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )
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30
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121
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42
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122 catMsg( c( " There are ", sampleCount, " samples found in input list") )
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123
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124 for ( sample in sampleNames ){
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42
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125 catMsg( c(" Working on sample ", sample ) )
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126 regionCount <- nrow( regionsList[[sample]] )
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127
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128 outSampleBase <- paste( outputBasename, '_', sample, '_QDNAseqRegions', sep='')
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129 outBedgraphFile <- paste( outSampleBase, '.bedGraph', sep="" )
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130 outBedgraphPath <- paste( outputDir, '/', outBedgraphFile, sep="" )
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131
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132 ## ---------- BEDGRAPH ----------
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133 txt <- paste( "track type=bedGraph color=0,100,0 altColor=255,0,0 name=", sample,"_segmReg description=segmented_regions_from_QDNAseq\n", sep="")
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134 sink( outBedgraphPath )
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135 cat( txt )
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136 sink()
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137 write.table( regionsList[[sample]][,bedgraphColumns], outBedgraphPath, quote=F, sep="\t", row.names=F, append=T, col.names=F)
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138 outFiles[[sample]] <- c( outBedgraphFile )
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139 }
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140 outFiles
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141 }
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142
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143 ## ==================================================
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144 ## Start of analysis
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145 ## ==================================================
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42
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146 MAIN_NAME <- '[INFO] '
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147 TOOL_PATH <- getScriptPath()
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148 CSS_FILE <- paste( TOOL_PATH, '/QDNAseq.css', sep="" )
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149 DECIMALS <- 3
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150 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
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151 PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
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152 PAR_SET <- list( pch=22 )
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153
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154 catMsg( "Starting QDNAseq wrapper" )
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155 catMsg( "Loading R libraries" )
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156 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
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157 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
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25
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158
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2
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159 ## only one param: the tmp config file
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160 cmdLineArgs <- commandArgs(TRUE)
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161 config <- cmdLineArgs[1]
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162
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163 ## sourcing the config file will load all input params
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59
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164 ## many variables are imported via sourced "config"
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165 source( config )
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166
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167 PLOT_RES <- min( PLOT_WIDTH, PLOT_HEIGHT ) / 6.3 # desparate try to make png text scale well, damn you R...!
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168 if ( doOutputCallsRds == TRUE ){ doCall <- TRUE }
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169
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170 systemUser <- system("whoami",T)
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171 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
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172 rVersion <- R.version.string
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173 catMsg( c("Analysis run with user: ", systemUser ) )
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174 catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) )
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59
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175 catMsg( c( rVersion ) )
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42
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176
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177 ## get the comma separated list of chromosomes to exclude
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178 excludeChrs <- unlist( strsplit( excludeChrsString, ",") )
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179
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180 ## ------------------------
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181 ## DEBUG
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182 #catMsg( "PARAM" )
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183 #catMsg( galaxy_path )
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184 #catMsg( repos_path )
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185 #catMsg( instal_path )
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186 ## /DEBUG
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187 ## ------------------------
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188
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59
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189 ## help msg for running script without wrapper still needs work!
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190 #if ( length(cmdLineArgs) == 0 || cmdLineArgs[1] == "-h" || cmdLineArgs[1] == "--help"){
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42
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191 # catMsg( c( "Usage: ", paste(params_help,sep=",") ) )
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192 # quit( save = 'no', status=0, runLast=F )
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193 #}
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194
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195 if ( !file.exists( outputPath) ){
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196 dir.create( outputPath )
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197 }
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198
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199 ## because we circumvent params that galaxy can save, we want to
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200 ## copy source config file to output dir to include it in output zip
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201 file.copy( config, paste(outputPath, 'qdnaseq_config_file.R', sep='/') )
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202
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203 ## ------------------------
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204 ## construct output file-names and -paths
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205 ## ------------------------
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206 htmlOutputName <- 'index.html'
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207 gzipOutputName <- paste( 'QDNAseqResults_', binSize, 'kbp_', outputName, '.zip', sep='' )
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208 robjReadCoName <- paste( binSize, 'kbp_QDNAseqReadCounts.rds', sep='')
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209 robjCopyNrName <- paste( binSize, 'kbp_QDNAseqCopyNumbers.rds', sep='')
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210 robjCalledName <- paste( binSize, 'kbp_QDNAseqCalledSegments.rds', sep='')
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211 regiOutputName <- paste( binSize, 'kbp_QDNAseqRegions.rds', sep='')
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212 igvCopyNrName <- paste( binSize, 'kbp_QDNAseq-normalized.igv', sep='')
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213 noiseImgName <- paste( 'QDNAseqNoisePlot.png', sep='')
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214 freqImgName <- paste( 'QDNAseqFrequencyPlot.png', sep='')
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215
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216 gzipOutputPath <- paste( outputPath, '/', gzipOutputName, sep='')
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217 htmlOutputPath <- paste( outputPath, '/', htmlOutputName, sep='')
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218 robjReadCoPath <- paste( outputPath, '/', robjReadCoName, sep='')
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219 robjCopyNrPath <- paste( outputPath, '/', robjCopyNrName, sep='')
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220 robjCalledPath <- paste( outputPath, '/', robjCalledName, sep='')
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221 robjRegionPath <- paste( outputPath, '/', regiOutputName, sep='')
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222 igvCopyNrPath <- paste( outputPath, '/', igvCopyNrName, sep='')
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223 noiseImgPath <- paste( outputPath, '/', noiseImgName, sep='' )
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224 freqImgPath <- paste( outputPath, '/', freqImgName, sep='' )
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225
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226 ## setup bam filelist for easy retrieval later
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227 fileList <- makeBamFileList( bamsPaths, bamsNames )
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228 bamCount <- length( fileList[[ 'all_paths' ]] )
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229
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230 ## ------------------------
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231 ## performing QDNAseq analysis steps
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232 ## ------------------------
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233 if ( debug ){ ## in case of debug just use inbuilt LGG data for speedup
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234 data(LGG150)
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235 readCounts <- LGG150
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236 binSize <- 15
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237 bamsPaths <- c( "BUILD_IN_DATA_LGG150")
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238 bamsNames <- c( "LGG150")
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239 fileList <- makeBamFileList( bamsPaths, bamsNames )
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240 bamCount <- length( fileList[[ 'all_paths' ]] )
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241 }else{
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242 if ( nchar(binAnnotations) == 0 ){
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243 binAnnotations <- getBinAnnotations( binSize=binSize, type=experimentType )
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244 }else{
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245 ## if user provided file, check if correct class
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246 if ( class(binAnnotations)[1] != 'AnnotatedDataFrame' ){
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247 stop( "Provided binAnnotations file is not of class 'AnnotatedDataFrame'\n" )
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248 }
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249 binAnnotations <- readRDS( binAnnotations )
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250 }
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251 ## provide bamnames because in galaxy everyting is called "dataset_###"
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252 readCounts <- binReadCounts( binAnnotations, bamfiles=fileList[[ 'all_paths' ]], bamnames=bamsNames )
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253 }
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254
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255 readCountsFiltered <- applyFilters( readCounts, residual=TRUE, blacklist=filterBlacklistedBins, mappability=mappabilityCutoff, chromosomes=excludeChrs )
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256 readCountsFiltered <- estimateCorrection( readCountsFiltered )
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257 copyNumbers <- correctBins( readCountsFiltered )
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258 copyNumbersNormalized <- normalizeBins( copyNumbers )
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259 copyNumbersSmooth <- smoothOutlierBins( copyNumbersNormalized )
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260 sampleNames <- readCountsFiltered@phenoData@data$name
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261
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262 ## save objects to output dir
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263 saveRDS( readCountsFiltered, robjReadCoPath );
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264 saveRDS( copyNumbersSmooth, robjCopyNrPath );
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265 exportBins( copyNumbersSmooth, file=igvCopyNrPath, format="igv" )
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266
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267 ## also save objects for galaxy history output if requested
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268 if ( doOutputReadcountsRds ){
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269 saveRDS( readCountsFiltered, readCountsDatasetFile );
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270 }
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271 if ( doOutputCopynumbersRds ){
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272 saveRDS( copyNumbersSmooth, copyNumbersDatasetFile );
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273 }
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274 if ( doOutputCopynumbersIgv ){
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275 saveRDS( copyNumbersSmooth, copyNumbersIgvDatasetFile );
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276 }
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277
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278 ## proceed with calling if requested
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279 if ( doCall ){
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280 copyNumbersSegmented <- segmentBins( copyNumbersSmooth, undo.splits=undoSplits, undo.SD=undoSD )
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281 copyNumbersSegmented <- normalizeSegmentedBins( copyNumbersSegmented )
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282 copyNumbersCalled <- callBins( copyNumbersSegmented )
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283 cgh <- makeCgh( copyNumbersCalled )
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284 saveRDS( copyNumbersCalled, robjCalledPath );
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285 if ( doOutputCallsRds ){
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286 saveRDS( copyNumbersCalled, calledSegmentsDatasetFile );
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287 }
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288 ## actual calls are not included in exportBins output, so not used now
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289 #exportBins( copyNumbersCalled, file=igvCalledPath, format="igv")
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290 }
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291
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292
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293
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294 ## ------------------------
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295 ## create output files
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296 ## ------------------------
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297 plotted_images <- list() # to keep track of images for later linking
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298 regions <- list() # will contain the (called) segments
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299
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300 png( noiseImgPath, width=PLOT_HEIGHT, height=PLOT_HEIGHT, res=PLOT_RES );
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301 par( PAR_SET )
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302 noisePlot( readCountsFiltered, col="darkgreen" )
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303 dev.off()
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304
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305 if ( doCall ){
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306 png( freqImgPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES );
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307 par( PAR_SET )
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308 frequencyPlot( copyNumbersCalled )
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309 dev.off()
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310 }
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311
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312 for (i in 1:length(sampleNames) ){
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313 sample <- sampleNames[i]
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314 usedReads <- readCountsFiltered@phenoData@data$used.reads[i]
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315 catMsg( c("Creating plots for sample: ", sample ) )
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316
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317 type <- 'CopyNumbers'
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318 img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png', sep='')
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319 img_file_path <- paste( outputPath, '/', img_file, sep='' )
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320 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES );
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321 par( PAR_SET )
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322 plot( copyNumbersSmooth[ ,sample ] );
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323 dev.off()
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324 plotted_images[[ sample ]][[ type ]] <- img_file
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325
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326 if ( doCall ){
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327 type <- 'Called'
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328 img_file <- paste( sample, '_', binSize, 'kbp_QDNAseq', type, '.png', sep='')
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329 img_file_path <- paste( outputPath, '/', img_file, sep='' )
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330 png( img_file_path, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES );
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331 par( PAR_SET )
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332 plot( copyNumbersCalled[ ,sample ] );
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333 dev.off()
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334 plotted_images[[ sample ]][[ type ]] <- img_file
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335
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42
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336 catMsg( c(" Fusing regions of sample: ", sample) )
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337 regions[[ sample ]] <- fuseRegions( cgh[, sample] )
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2
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338 region_count <- nrow( data.frame( regions[[ sample ]] ) )
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42
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339 catMsg( c( ' sample "', sample, '" has ', region_count, " regions" ) )
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2
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340 plotted_images[[ sample ]][[ 'region_count' ]] <- region_count
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341 }
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342
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30
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343 ## add USED read counts
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2
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344 plotted_images[[ sample ]][[ 'usedReads' ]] <- usedReads
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345 }
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346
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347 if ( doCall ){
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348 saveRDS( regions, robjRegionPath )
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349 printedFiles <- outputRegionsFromList( regions, outputBasename=outputName, outputDir=outputPath )
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350 }
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351
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352 ## ------------------------
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353 ## prepare output
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354 ## ------------------------
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42
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355 catMsg( "...zipping output")
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2
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356 zip_cmd <- paste( "zip -j", gzipOutputPath, paste(outputPath,'/*',sep='') ) ## -j is for removing dirs from the tree
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357 system( zip_cmd )
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358
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359 ## ------------------------
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360 ## get filesizes for report
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361 ## ------------------------
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59
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362 zippedSize <- paste( round( file.info( gzipOutputPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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363 readCoSize <- paste( round( file.info( robjReadCoPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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364 copyNrSize <- paste( round( file.info( robjCopyNrPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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365 calledSize <- paste( round( file.info( robjCalledPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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366 regionSize <- paste( round( file.info( robjRegionPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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367 igvCopyNrSize <- paste( round( file.info( igvCopyNrPath )[["size"]] / 1e+6, digits=2 ), 'MB' )
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2
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368
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369 ## ------------------------
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370 ## creating html output to be linked to from the middle galaxy pane
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371 ## ------------------------
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372
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373 #sink( file = outputHtml, type = "output" )
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374 sink( file = htmlOutputPath, type = "output" )
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375 cat( "<html>\n")
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376 cat( "<head>\n")
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377 #cat( '<link rel="stylesheet" type="text/css" href="test.css" media="screen" />', "\n" )
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59
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378 cat( "\t", '<title>QDNAseq Report | ', outputName,'</title>', "\n", sep='' )
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379 cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )
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380 cat( "\t<style>\n", sep='')
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381 ## include CSS into html file, makes it more portable
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382 cat( paste( "\t\t", '/* the css here originates from ', CSS_FILE,' */', "\n"), sep='' )
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383 cat( "\t\t", readLines( CSS_FILE ), sep="\n\t\t" )
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2
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384 #cat( "\t\th1 {color:red;}", "\n")
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59
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385 cat( "\n\t</style>\n" )
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2
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386
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387 cat( "\n</head>\n")
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388 cat( "\n<body>\n")
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389
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390 cat( "<h1>QDNAseq Report</h1>", "\n")
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391
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392 cat( '<h3 class="qdnaseq">About this analysis</h3>', "\n")
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59
|
393 cat( '<p>This page provides access to all results. To have a local copy of this report just download the <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep='')
|
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2
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394
|
|
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395 ## ------------------------
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396 ## table with general info
|
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397 ## ------------------------
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|
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398 cat( '<h3 class="qdnaseq">Settings</h3><p>', "\n")
|
|
59
|
399 cat( '<table class="pure-table pure-table-striped"><tbody>' )
|
|
2
|
400 cat( htmlTableRow( c( "AnalysisName", outputName ) ) )
|
|
59
|
401 cat( htmlTableRow( c( "AnalysisDate", as.character(Sys.time()) ) ) )
|
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2
|
402 cat( htmlTableRow( c( "BinSize (kb)", binSize ) ) )
|
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59
|
403 cat( htmlTableRow( c( "R info", rVersion ) ) )
|
|
|
404 cat( htmlTableRow( c( "QDNAseq info", qdnaseqVersion ) ) )
|
|
2
|
405
|
|
59
|
406 sampleStrings <- c()
|
|
2
|
407 for ( galaxyName in fileList[[ 'all_files' ]] ){
|
|
|
408 sampleName <- fileList[[ galaxyName ]]
|
|
59
|
409 sampleStrings <- c( sampleStrings, paste( galaxyName, ' (', sampleName, ')', sep='' ) )
|
|
2
|
410 }
|
|
59
|
411 cat( htmlTableRow( c( "InputBams", paste( sampleStrings, collapse=", ") ) ) )
|
|
|
412
|
|
2
|
413 cat( "</tbody></table></p>", "\n")
|
|
|
414
|
|
|
415 ## ------------------------
|
|
|
416 ## list with links to all output files
|
|
|
417 ## ------------------------
|
|
59
|
418
|
|
2
|
419
|
|
|
420 cat( '<h3 class="qdnaseq">Output files</h3><p>', "\n")
|
|
|
421 cat( '<dl>', "\n" )
|
|
|
422 cat( '<dt>', htmlLink( path=robjReadCoName, robjReadCoName ), '</dt>', "\n" )
|
|
|
423 cat( '<dd>QDNAseq object with read counts per bin, ', readCoSize,'</dd>', "\n" )
|
|
59
|
424
|
|
2
|
425
|
|
|
426 cat( '<dt>', htmlLink( path=robjCopyNrName, robjCopyNrName ), '</dt>', "\n" )
|
|
|
427 cat( '<dd>QDNAseq object with copy numbers per bin, ', copyNrSize,'</dd>', "\n" )
|
|
|
428
|
|
31
|
429 cat( '<dt>', htmlLink( path=igvCopyNrName, igvCopyNrName ), '</dt>', "\n" )
|
|
|
430 cat( '<dd>IGV formatted text file with copy numbers per bin, ', igvCopyNrSize,'</dd>', "\n" )
|
|
|
431
|
|
2
|
432 if ( doCall ){
|
|
|
433 cat( '<dt>', htmlLink( path=robjCalledName, robjCalledName ), '</dt>', "\n" )
|
|
|
434 cat( '<dd>QDNAseq object with segment and call status per bin, ', calledSize,'</dd>', "\n" )
|
|
|
435
|
|
|
436 cat( '<dt>', htmlLink( path=regiOutputName, regiOutputName ), '</dt>', "\n" )
|
|
|
437 cat( '<dd>list with segmented/called regions for each sample, ', regionSize, '</dd>', "\n" )
|
|
|
438 }
|
|
|
439 cat( '</dl></p>', "\n" )
|
|
|
440
|
|
59
|
441 r_code <- '## start own downstream analysis in R with:'
|
|
|
442 r_code <- c( r_code, 'library( QDNAseq )' )
|
|
|
443 r_code <- c( r_code, paste( 'readRDS( ', robjReadCoName, ' ) -> readCounts', sep="") )
|
|
|
444
|
|
42
|
445 ## r_code shows example code on how to load output files
|
|
25
|
446 #cat( r_code, "</p>\n", sep="\n")
|
|
2
|
447 cat( '<p>See ', htmlLink( WEB_LINK, 'the bioconductor QDNAseq documentation' ), ' for more information on how to work with these files</p>', "\n", sep='' )
|
|
59
|
448 cat( '<pre>', paste( r_code, collapse="\n" ), '</pre>', "\n", sep='' )
|
|
2
|
449
|
|
|
450 ## ------------------------
|
|
|
451 ## table with links to files
|
|
|
452 ## ------------------------
|
|
|
453 cat( '<h3 class="qdnaseq">Results: overview</h3><p>', "\n")
|
|
|
454 plots_html <- ''
|
|
|
455
|
|
40
|
456 cat( '<table class="pure-table pure-table-striped"><thead><tr><th>Sample / File</th><th>CopyNr</th><th>Calls</th><th>Reads</th><th>Regions</th><th>Files</th></tr></thead><tbody>' )
|
|
2
|
457
|
|
|
458 for ( bam_file in sampleNames ){
|
|
|
459
|
|
|
460 #width <- 600; height <- 240
|
|
|
461 width <- PLOT_WIDTH; height <- PLOT_HEIGHT
|
|
|
462 width_t <- 100; height_t <- 40
|
|
|
463
|
|
|
464 ## add thumbnails to table with links to anchors on html page
|
|
|
465 copy_img <- plotted_images[[ bam_file ]][[ 'CopyNumbers' ]]
|
|
|
466 usedReads <- plotted_images[[ bam_file ]][[ 'usedReads' ]]
|
|
|
467 usedReads <- format( as.integer(usedReads), digits=4, decimal.mark=".", big.mark="," )
|
|
|
468
|
|
|
469 html_copy_thumb <- htmlLink( path=paste('#', copy_img, sep=''), paste('<img src="',copy_img,'" alt="', bam_file, '" width="', width_t, '" height="', height_t, '">', sep='') )
|
|
|
470 html_copy_img <- htmlLink( path=copy_img, paste('<img id="', copy_img,'" src="',copy_img,'" alt="',bam_file, '" width="', width, '" height="', height, '">', sep='') )
|
|
|
471 html_call_thumb <- 'NA'
|
|
|
472 html_call_img <- ''
|
|
|
473 html_bedGraph <- 'NA'
|
|
|
474 region_count <- 'NA'
|
|
|
475
|
|
|
476 if ( doCall ){
|
|
|
477 call_img <- plotted_images[[ bam_file ]][[ 'Called' ]]
|
|
|
478 region_count <- plotted_images[[ bam_file ]][[ 'region_count' ]]
|
|
|
479 html_call_thumb <- htmlLink( path=paste('#', call_img, sep=''), paste('<img src="', call_img, '" alt="', bam_file, '" width="', width_t,'" height="', height_t,'">', sep='') )
|
|
|
480
|
|
59
|
481 ## list structure with output files just is an array per BAM
|
|
|
482 html_bedGraph <- htmlLink( path=printedFiles[[ bam_file ]][1], 'bedGraph' )
|
|
2
|
483 html_call_img <- htmlLink( path=call_img, paste('<img id="', call_img,'" src="', call_img,'" alt="', bam_file, '" width="', width, '" height="', height,'">', sep='') )
|
|
|
484 }
|
|
|
485
|
|
|
486 ## add info to overview table, including small thumbnails
|
|
59
|
487 cat( htmlTableRow( c(bam_file, html_copy_thumb, html_call_thumb, usedReads, region_count, paste( html_bedGraph, sep=", ")) ), "\n" )
|
|
2
|
488 ## now include (large) images in html page
|
|
|
489 plots_html <- paste( plots_html, html_copy_img, "\n", html_call_img, "\n<hr \\>\n", sep='' )
|
|
|
490 }
|
|
|
491 cat( "</tbody></table></p>", "\n")
|
|
|
492
|
|
42
|
493 ## ------------------------
|
|
|
494 ## create the noise and frequency plots
|
|
|
495 ## ------------------------
|
|
|
496 html_noise_img <- htmlLink(
|
|
|
497 path=noiseImgName,
|
|
55
|
498 paste('<img id="', noiseImgName,'" src="', noiseImgName, '" width="', height/2, '" height="', height/2, '" alt="NoisePlot">', sep='')
|
|
42
|
499 )
|
|
|
500 html_freq_img <- htmlLink(
|
|
|
501 path=freqImgName,
|
|
55
|
502 paste('<img id="', freqImgName,'" src="', freqImgName, '" width="', width/2, '" height="', height/2, ' alt="FrequenceyPlot">', sep='')
|
|
42
|
503 )
|
|
56
|
504 ## there only is a frequency plot when data is called
|
|
|
505 if ( !doCall ){ html_freq_img <- '' }
|
|
59
|
506
|
|
|
507 extra_plots_html <- paste( html_noise_img, " \n", html_freq_img, "\n", sep='' )
|
|
2
|
508
|
|
|
509 ## ------------------------
|
|
|
510 ## section with various output shown
|
|
|
511 ## ------------------------
|
|
42
|
512 cat( '<h3 class="qdnaseq">Results: Analysis plots</h3><p>', "\n")
|
|
|
513 cat( extra_plots_html, "\n")
|
|
|
514 cat( '<h3 class="qdnaseq">Results: Sample plots</h3><p>', "\n")
|
|
2
|
515 cat( plots_html, "\n")
|
|
|
516 cat( "\n</p></body>\n")
|
|
|
517 cat( "\n</html>\n")
|
|
|
518 sink()
|
|
|
519
|
|
|
520 ## ------------------------
|
|
42
|
521 ## creating main html output for galaxy history
|
|
2
|
522 ## ------------------------
|
|
|
523 sink( file = outputHtml, type = "output" )
|
|
|
524
|
|
|
525 cat( "<head>", "\n")
|
|
59
|
526 cat( "\t", '<link rel="stylesheet" href="', PURE_CSS, '">', "\n", sep='' )
|
|
2
|
527
|
|
|
528 cat( "<style>", "\n")
|
|
42
|
529 ## include CSS directly into html file
|
|
2
|
530 cat( paste( "\t", '/* the css here originates from ', CSS_FILE,' */', "\n") )
|
|
|
531 cat( paste( "\t", readLines( CSS_FILE, n = -1)), sep="\n" )
|
|
|
532 cat( "</style>", "\n")
|
|
|
533 cat( "</head>", "\n")
|
|
|
534
|
|
|
535 cat( '<h1>QDNAseq Results (', outputName,')</h1>', "\n", sep="")
|
|
59
|
536 cat( '<p>Explore <a href="', htmlOutputName, '" class="button">the results</a> directly within galaxy</p>', "\n", sep="")
|
|
|
537 cat( '<p>Or download a <a href="', gzipOutputName, '" class="button">zipfile</a> with all output (', zippedSize, ')</p>', "\n", sep="" )
|
|
2
|
538
|
|
|
539 cat( '<p>The zip file contains all output files, including *.rds files allowing you to load the R copyNumber object(s) and perform further detailed analysis or create your own output for further processing. You can load the rds file with <code class="code">loadRDS(file.rds)</code></p>', "\n", sep="")
|
|
|
540
|
|
|
541 sink()
|
|
|
542
|
|
42
|
543 ## ------------------------
|
|
|
544 ## create final zip and quit with status 0 to tell galaxy all was fine
|
|
|
545 ## ------------------------
|
|
|
546 catMsg( "zipping all output")
|
|
|
547 system( paste( "zip -j ", gzipOutputPath, paste(outputPath,'/', htmlOutputName, sep='') ) )
|
|
|
548 catMsg( "done" )
|
|
25
|
549 q(status=0)
|
