Mercurial > repos > davidvanzessen > report_clonality_tcell_igg
changeset 2:fd1b76816395 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 27 Mar 2014 10:54:03 -0400 |
| parents | 1ba88ffd6f4e |
| children | b850200d4335 |
| files | RScript.r asc.gif bg.gif desc.gif jquery-1.11.0.min.js jquery.tablesorter.min.js plotting_merged.xml r_wrapper.sh script.js style.css |
| diffstat | 10 files changed, 224 insertions(+), 50 deletions(-) [+] |
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--- a/RScript.r Tue Mar 11 11:13:33 2014 -0400 +++ b/RScript.r Thu Mar 27 10:54:03 2014 -0400 @@ -6,7 +6,6 @@ outFile = args[2] outDir = args[3] clonalType = args[4] -species = args[5] if (!("gridExtra" %in% rownames(installed.packages()))) { install.packages("gridExtra", repos="http://cran.xl-mirror.nl/") @@ -26,11 +25,18 @@ } library(data.table) +if (!("reshape2" %in% rownames(installed.packages()))) { + install.packages("reshape2", repos="http://cran.xl-mirror.nl/") +} +library(reshape2) + test = read.table(inFile, sep="\t", header=TRUE, fill=T, comment.char="") test = test[test$Sample != "",] + + test$Top.V.Gene = gsub("[*]([0-9]+)", "", test$Top.V.Gene) test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene) test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene) @@ -50,23 +56,31 @@ PRODF = PROD #PRODF = unique(PRODF) -PRODF = PRODF[!duplicated(PRODF$VDJCDR3), ] +if(any(grepl(pattern="_", x=PRODF$ID))){ -PRODFV = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Sample", "Top.V.Gene")]) + PRODF$freq = gsub("^[0-9]+_", "", PRODF$ID) + PRODF$freq = gsub("_.*", "", PRODF$freq) + PRODF$freq = as.numeric(PRODF$freq) +} else { + PRODF$freq = 1 + PRODF = PRODF[!duplicated(PRODF$VDJCDR3), ] +} + +PRODFV = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Sample", "Top.V.Gene")]) PRODFV$Length = as.numeric(PRODFV$Length) Total = 0 Total = ddply(PRODFV, .(Sample), function(x) data.frame(Total = sum(x$Length))) PRODFV = merge(PRODFV, Total, by.x='Sample', by.y='Sample', all.x=TRUE) PRODFV = ddply(PRODFV, c("Sample", "Top.V.Gene"), summarise, relFreq= (Length*100 / Total)) -PRODFD = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Sample", "Top.D.Gene")]) +PRODFD = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Sample", "Top.D.Gene")]) PRODFD$Length = as.numeric(PRODFD$Length) Total = 0 Total = ddply(PRODFD, .(Sample), function(x) data.frame(Total = sum(x$Length))) PRODFD = merge(PRODFD, Total, by.x='Sample', by.y='Sample', all.x=TRUE) PRODFD = ddply(PRODFD, c("Sample", "Top.D.Gene"), summarise, relFreq= (Length*100 / Total)) -PRODFJ = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Sample", "Top.J.Gene")]) +PRODFJ = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Sample", "Top.J.Gene")]) PRODFJ$Length = as.numeric(PRODFJ$Length) Total = 0 Total = ddply(PRODFJ, .(Sample), function(x) data.frame(Total = sum(x$Length))) @@ -94,11 +108,12 @@ setwd(outDir) -write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=F,col.names=T) +write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T) pV = ggplot(PRODFV) pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage") +write.table(x=PRODFV, file="VFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) png("VPlot.png",width = 1280, height = 720) pV @@ -107,6 +122,7 @@ pD = ggplot(PRODFD) pD = pD + geom_bar( aes( x=factor(reorder(Top.D.Gene, chr.orderD)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) pD = pD + xlab("Summary of D gene") + ylab("Frequency") + ggtitle("Relative frequency of D gene usage") +write.table(x=PRODFD, file="DFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) png("DPlot.png",width = 800, height = 600) pD @@ -115,18 +131,76 @@ pJ = ggplot(PRODFJ) pJ = pJ + geom_bar( aes( x=factor(reorder(Top.J.Gene, chr.orderJ)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1)) pJ = pJ + xlab("Summary of J gene") + ylab("Frequency") + ggtitle("Relative frequency of J gene usage") +write.table(x=PRODFJ, file="JFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) png("JPlot.png",width = 800, height = 600) pJ dev.off(); +VGenes = PRODF[,c("Sample", "Top.V.Gene", "freq")] +VGenes$Top.V.Gene = gsub("-.*", "", VGenes$Top.V.Gene) +VGenes = data.frame(data.table(VGenes)[, list(Count=sum(freq)), by=c("Sample", "Top.V.Gene")]) +TotalPerSample = data.frame(data.table(VGenes)[, list(total=sum(.SD$Count)), by=Sample]) +VGenes = merge(VGenes, TotalPerSample, by="Sample") +VGenes$Frequency = VGenes$Count * 100 / VGenes$total +VPlot = ggplot(VGenes) +VPlot = VPlot + geom_bar(aes( x = Top.V.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of V gene families") + + ylab("Percentage of sequences") +png("VFPlot.png") +VPlot +dev.off(); +write.table(x=VGenes, file="VFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) + +DGenes = PRODF[,c("Sample", "Top.D.Gene", "freq")] +DGenes$Top.D.Gene = gsub("-.*", "", DGenes$Top.D.Gene) +DGenes = data.frame(data.table(DGenes)[, list(Count=sum(freq)), by=c("Sample", "Top.D.Gene")]) +TotalPerSample = data.frame(data.table(DGenes)[, list(total=sum(.SD$Count)), by=Sample]) +DGenes = merge(DGenes, TotalPerSample, by="Sample") +DGenes$Frequency = DGenes$Count * 100 / DGenes$total +DPlot = ggplot(DGenes) +DPlot = DPlot + geom_bar(aes( x = Top.D.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of D gene families") + + ylab("Percentage of sequences") +png("DFPlot.png") +DPlot +dev.off(); +write.table(x=DGenes, file="DFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) + +JGenes = PRODF[,c("Sample", "Top.J.Gene", "freq")] +JGenes$Top.J.Gene = gsub("-.*", "", JGenes$Top.J.Gene) +JGenes = data.frame(data.table(JGenes)[, list(Count=sum(freq)), by=c("Sample", "Top.J.Gene")]) +TotalPerSample = data.frame(data.table(JGenes)[, list(total=sum(.SD$Count)), by=Sample]) +JGenes = merge(JGenes, TotalPerSample, by="Sample") +JGenes$Frequency = JGenes$Count * 100 / JGenes$total +JPlot = ggplot(JGenes) +JPlot = JPlot + geom_bar(aes( x = Top.J.Gene, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Distribution of J gene families") + + ylab("Percentage of sequences") +png("JFPlot.png") +JPlot +dev.off(); +write.table(x=JGenes, file="JFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) + +CDR3Length = data.frame(data.table(PRODF)[, list(Count=sum(freq)), by=c("Sample", "CDR3.Length.DNA")]) +TotalPerSample = data.frame(data.table(CDR3Length)[, list(total=sum(.SD$Count)), by=Sample]) +CDR3Length = merge(CDR3Length, TotalPerSample, by="Sample") +CDR3Length$Frequency = CDR3Length$Count * 100 / CDR3Length$total +CDR3LengthPlot = ggplot(CDR3Length) +CDR3LengthPlot = CDR3LengthPlot + geom_bar(aes( x = CDR3.Length.DNA, y = Frequency, fill = Sample), stat='identity', position='dodge' ) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) + + ggtitle("Length distribution of CDR3") + + xlab("CDR3 Length") + + ylab("Percentage of sequences") +png("CDR3LengthPlot.png",width = 1280, height = 720) +CDR3LengthPlot +dev.off() +write.table(x=CDR3Length, file="CDR3LengthPlot.csv", sep=",",quote=F,row.names=F,col.names=T) + revVchain = Vchain revDchain = Dchain revVchain$chr.orderV = rev(revVchain$chr.orderV) revDchain$chr.orderD = rev(revDchain$chr.orderD) -cat("before VD", "\n") - plotVD <- function(dat){ if(length(dat[,1]) == 0){ return() @@ -141,10 +215,12 @@ png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) + dev.off() + write.table(x=acast(dat, Top.V.Gene~Top.D.Gene, value.var="Length"), file=paste("HeatmapVD_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) } -VandDCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.D.Gene", "Sample")]) +VandDCount = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Top.V.Gene", "Top.D.Gene", "Sample")]) VandDCount$l = log(VandDCount$Length) maxVD = data.frame(data.table(VandDCount)[, list(max=max(l)), by=c("Sample")]) @@ -160,9 +236,7 @@ lapply(VDList, FUN=plotVD) -cat("after VD", "\n") -cat("before VJ", "\n") plotVJ <- function(dat){ if(length(dat[,1]) == 0){ @@ -179,9 +253,10 @@ png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name))) print(img) dev.off() + write.table(x=acast(dat, Top.V.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapVJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) } -VandJCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.J.Gene", "Sample")]) +VandJCount = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Top.V.Gene", "Top.J.Gene", "Sample")]) VandJCount$l = log(VandJCount$Length) maxVJ = data.frame(data.table(VandJCount)[, list(max=max(l)), by=c("Sample")]) @@ -196,10 +271,6 @@ VJList = split(completeVJ, f=completeVJ[,"Sample"]) lapply(VJList, FUN=plotVJ) -cat("after VJ", "\n") - -cat("before DJ", "\n") - plotDJ <- function(dat){ if(length(dat[,1]) == 0){ return() @@ -215,6 +286,7 @@ png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name))) print(img) dev.off() + write.table(x=acast(dat, Top.D.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapDJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) } DandJCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.D.Gene", "Top.J.Gene", "Sample")]) @@ -232,7 +304,6 @@ DJList = split(completeDJ, f=completeDJ[,"Sample"]) lapply(DJList, FUN=plotDJ) -cat("after DJ", "\n") sampleFile <- file("samples.txt") un = unique(test$Sample) @@ -241,27 +312,26 @@ close(sampleFile) - if("Replicate" %in% colnames(test)) { clonalityFrame = PROD clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":")) clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ] - write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=F,col.names=T) + write.table(clonalityFrame, "clonalityComplete.csv", sep=",",quote=F,row.names=F,col.names=T) ClonalitySampleReplicatePrint <- function(dat){ - write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) } clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) - lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) + #lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) ClonalitySamplePrint <- function(dat){ - write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(dat, paste("clonality_", unique(dat$Sample) , ".csv", sep=""), sep=",",quote=F,row.names=F,col.names=T) } clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) - lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) + #lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) clonalFreq = data.frame(data.table(clonalityFrame)[, list(Type=.N), by=c("Sample", "VDJCDR3")]) clonalFreqCount = data.frame(data.table(clonalFreq)[, list(Count=.N), by=c("Sample", "Type")])
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotting_merged.xml Thu Mar 27 10:54:03 2014 -0400 @@ -0,0 +1,23 @@ +<tool id="report_clonality_igg" name="Report Clonality" version="1.0"> + <description> </description> + <command interpreter="bash"> + r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" + </command> + <inputs> + <param name="in_file" format="tabular" type="data" label="Data to Process" /> + <param name="clonaltype_select" type="select" label="Clonal Type Definition"> + <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> + <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> + <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> + <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option> + </param> + + </inputs> + <outputs> + <data format="html" name="out_file" /> + </outputs> + <help> + Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J) + </help> +</tool>
--- a/r_wrapper.sh Tue Mar 11 11:13:33 2014 -0400 +++ b/r_wrapper.sh Thu Mar 27 10:54:03 2014 -0400 @@ -4,15 +4,30 @@ outputDir=$3 outputFile=$3/index.html #$2 clonalType=$4 -species=$5 dir="$(cd "$(dirname "$0")" && pwd)" mkdir $3 -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1 +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 cp $dir/tabber.js $outputDir cp $dir/style.css $outputDir cp $dir/script.js $outputDir +cp $dir/jquery-1.11.0.min.js $outputDir +cp $dir/jquery.tablesorter.min.js $outputDir +cp $dir/asc.gif $outputDir +cp $dir/desc.gif $outputDir +cp $dir/bg.gif $outputDir echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $2 -echo "<html><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'><div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile +echo "<html<head>" >> $outputFile +echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile +echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile +echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile +echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile +echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile +echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile + +echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile +echo "<img src='VFPlot.png'/>" >> $outputFile +echo "<img src='DFPlot.png'/>" >> $outputFile +echo "<img src='JFPlot.png'/>" >> $outputFile echo "<img src='VPlot.png'/>" >> $outputFile echo "<img src='DPlot.png'/>" >> $outputFile echo "<img src='JPlot.png'/></div>" >> $outputFile @@ -22,13 +37,9 @@ echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile for sample in $samples; do echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile - - mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" - echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" - echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile - mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" - echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile + echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile + echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile + echo "<td><img src='HeatmapDJ_$sample.png'/></td></tr></table></div>" >> $outputFile count=$((count+1)) done echo "</div></div>" >> $outputFile @@ -69,13 +80,15 @@ echo "</div></div>" >> $outputFile fi -if [[ "$hasReplicateColumn" == "Yes" ]] ; then - echo "<div class='tabbertab' title='Junction Analysis'><table border='1'><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th></tr>" >> $outputFile +hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" + +if [[ "$hasJunctionData" == "Yes" ]] ; then + echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP do echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile done < $outputDir/junctionAnalysis.csv - echo "</table></div>" >> $outputFile + echo "</tbody></table></div>" >> $outputFile fi echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile @@ -91,7 +104,24 @@ echo "<div class='tabbertab' title='Downloads'>" >> $outputFile echo "<table border='1'>" >> $outputFile echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile -echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.tsv'>Download</a></td></tr>" >> $outputFile -echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.tsv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile + +echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile + +echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the J gene family frequency graph</td><td><a href='JFFrequency.csv'>Download</a></td></tr>" >> $outputFile + +echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile + +for sample in $samples; do + echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile + echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile + echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile +done + echo "</table>" >> $outputFile -echo "</div>" >> $outputFile +echo "</div></html>" >> $outputFile
--- a/script.js Tue Mar 11 11:13:33 2014 -0400 +++ b/script.js Thu Mar 27 10:54:03 2014 -0400 @@ -1,32 +1,36 @@ function compareAdd(id){ var img = document.createElement('img'); - img.setAttribute('src', 'VD_' + id + '.png'); + img.setAttribute('src', 'HeatmapVD_' + id + '.png'); var td = document.createElement('td'); td.setAttribute('id', "comparison_vd_" + id); td.appendChild(img) - document.getElementById('comparison_table_vd').appendChild(td); + $('#comparison_table_vd').append(td); img = document.createElement('img'); - img.setAttribute('src', 'VJ_' + id + '.png'); + img.setAttribute('src', 'HeatmapVJ_' + id + '.png'); td = document.createElement('td'); td.setAttribute('id', "comparison_vj_" + id); td.appendChild(img) - document.getElementById('comparison_table_vj').appendChild(td); + $('#comparison_table_vj').append(td); img = document.createElement('img'); - img.setAttribute('src', 'DJ_' + id + '.png'); + img.setAttribute('src', 'HeatmapDJ_' + id + '.png'); td = document.createElement('td'); td.setAttribute('id', "comparison_dj_" + id); td.appendChild(img) - document.getElementById('comparison_table_dj').appendChild(td); + $('#comparison_table_dj').append(td); - document.getElementById('compare_checkbox_' + id).setAttribute('onchange', "javascript:compareRemove('" + id + "')"); + $('#compare_checkbox_' + id).attr('onchange', "javascript:compareRemove('" + id + "')"); } function compareRemove(id){ - document.getElementById("comparison_vd_" + id).remove() - document.getElementById("comparison_vj_" + id).remove() - document.getElementById("comparison_dj_" + id).remove() - document.getElementById('compare_checkbox_' + id).setAttribute('onchange', "javascript:compareAdd('" + id + "')"); + $("#comparison_vd_" + id).remove() + $("#comparison_vj_" + id).remove() + $("#comparison_dj_" + id).remove() + $("#compare_checkbox_" + id).attr('onchange', "javascript:compareAdd('" + id + "')"); } + +$( document ).ready(function () { + $('#junction_table').tablesorter(); +})
--- a/style.css Tue Mar 11 11:13:33 2014 -0400 +++ b/style.css Thu Mar 27 10:54:03 2014 -0400 @@ -108,4 +108,43 @@ overflow:auto; } +/* tables */ +table.tablesorter { + font-family:arial; + background-color: #CDCDCD; + margin:10px 0pt 15px; + font-size: 8pt; + width: 100%; + text-align: left; +} +table.tablesorter thead tr th, table.tablesorter tfoot tr th { + background-color: #e6EEEE; + border: 1px solid #FFF; + font-size: 8pt; + padding: 4px; +} +table.tablesorter thead tr .header { + background-image: url(bg.gif); + background-repeat: no-repeat; + background-position: center right; + cursor: pointer; +} +table.tablesorter tbody td { + color: #3D3D3D; + padding: 4px; + background-color: #FFF; + vertical-align: top; +} +table.tablesorter tbody tr.odd td { + background-color:#F0F0F6; +} +table.tablesorter thead tr .headerSortUp { + background-image: url(asc.gif); +} +table.tablesorter thead tr .headerSortDown { + background-image: url(desc.gif); +} +table.tablesorter thead tr .headerSortDown, table.tablesorter thead tr .headerSortUp { +background-color: #8dbdd8; +}