# HG changeset patch # User davidvanzessen # Date 1482339183 18000 # Node ID 5d11c9139a55d535cec30cad583abf502cf35e7d # Parent da95be204ebc3733df3730527a78f218c7afdb82 Uploaded diff -r da95be204ebc -r 5d11c9139a55 complete_immunerepertoire.xml --- a/complete_immunerepertoire.xml Wed Dec 21 05:57:31 2016 -0500 +++ b/complete_immunerepertoire.xml Wed Dec 21 11:53:03 2016 -0500 @@ -17,8 +17,8 @@ - - + + @@ -118,87 +118,70 @@ - The entire Immune Repertoire pipeline as a single tool, input several FASTA files or IMGT zip/txz files, give them an ID and it will BLAST/parse, merge and plot them. - - .. class:: warningmark + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/RScript.r --- a/report_clonality/RScript.r Wed Dec 21 05:57:31 2016 -0500 +++ b/report_clonality/RScript.r Wed Dec 21 11:53:03 2016 -0500 @@ -159,7 +159,7 @@ #write the complete dataset that is left over, will be the input if 'none' for clonaltype and 'no' for filterproductive write.table(PRODF, "allUnique.txt", sep="\t",quote=F,row.names=F,col.names=T) -write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T) +#write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T) write.table(UNPROD, "allUnproductive.csv", sep=",",quote=F,row.names=F,col.names=T) #write the samples to a file @@ -297,7 +297,7 @@ 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") + scale_fill_manual(values=sample.colors) pV = pV + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) -write.table(x=PRODFV, file="VFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) +write.table(x=PRODFV, file="VFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) png("VPlot.png",width = 1280, height = 720) pV @@ -308,7 +308,7 @@ 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") + scale_fill_manual(values=sample.colors) pD = pD + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) - write.table(x=PRODFD, file="DFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) + write.table(x=PRODFD, file="DFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) png("DPlot.png",width = 800, height = 600) print(pD) @@ -319,7 +319,7 @@ 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") + scale_fill_manual(values=sample.colors) pJ = pJ + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) -write.table(x=PRODFJ, file="JFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) +write.table(x=PRODFJ, file="JFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) png("JPlot.png",width = 800, height = 600) pJ @@ -344,7 +344,7 @@ png("VFPlot.png") VPlot dev.off(); -write.table(x=VGenes, file="VFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) +write.table(x=VGenes, file="VFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) if(useD){ DGenes = PRODF[,c("Sample", "Top.D.Gene")] @@ -362,7 +362,7 @@ png("DFPlot.png") print(DPlot) dev.off(); - write.table(x=DGenes, file="DFFrequency.csv", sep=",",quote=F,row.names=F,col.names=T) + write.table(x=DGenes, file="DFFrequency.txt", sep="\t",quote=F,row.names=F,col.names=T) } # ---------------------- Plotting the cdr3 length ---------------------- @@ -579,7 +579,7 @@ if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available { print("Report Clonality - Clonality") - write.table(clonalityFrame, "clonalityComplete.csv", sep=",",quote=F,row.names=F,col.names=T) + write.table(clonalityFrame, "clonalityComplete.txt", sep="\t",quote=F,row.names=F,col.names=T) if(clonality_method == "boyd"){ samples = split(clonalityFrame, clonalityFrame$Sample, drop=T) @@ -871,7 +871,7 @@ png("AAComposition.png",width = 1280, height = 720) AAfreqplot dev.off() -write.table(AAfreq, "AAComposition.csv" , sep=",",quote=F,na="-",row.names=F,col.names=T) +write.table(AAfreq, "AAComposition.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) # ---------------------- AA median CDR3 length ---------------------- diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_cdr3_char.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_cdr3_char.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,100 @@ + + + + + + + + + + + +
+ +

This tab gives information on the +different characteristics of the CDR3.

+ +

Graphs

+ +

length distribution of CDR3

+ +

Graph visualizing for each donor the +distribution of the CDR3 length in amino acids between all sequences.

+ + +

Amino acid composition of CDR3

+ +

Bar graph visualizing for each donor how +frequent each amino acid is used in the CDR3 of all sequences. The red colour +in the background indicate positively charged amino acids, and the blue colour +in the background indicate negatively charged amino acids. The amino acids are +ordered from hydrophilic (left) to hydrophobic (right).

+ +

D reading frame

+ +

Bar graph visualizing the frequency by +which each D reading frame is used in each donor.

+ +

Table

+ +

Table showing for each donor the median +CDR3 length.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_circos.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_circos.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,59 @@ + + + + + + + + + + + +
+ +

Martin Krzywinski, Jacqueline Schein, İnan +Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco +A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome +Research 10.1101/gr.092759.109.

+ +

Circos plot showing the V-D, V-J, and D-J gen usage. +The thicker the line the more frequent this gene combination is used.

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_clonality.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_clonality.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,67 @@ + + + + + + + + + + + +
+ +

For each donor a +subtab is provided containing information on the sequence overlap between +replicates of the different replicates of one donor. Dependent on the settings +of the Shared clonal types / clonality filter a clonality score is given. The clonality +score is calculated according to the formula described by Boyd +et al, PMID: 20161664.

+ +

For each +individual replicate the number of reads is reported. In addition, the number +of coincidences between the different replicates of the same donor are reported. +

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_compare.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_compare.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,61 @@ + + + + + + + + + + + +
+ +

The tab allows +you to compare the VD, VJ and DJ heatmaps of multiple donors to each other.

+ +

By ticking the include box of a donor, the three +heatmaps of this donor is visualized underneath eachother. By clicking the +include box of multiple samples the heatmaps of these samples are visualized +next to each other allowing easy comparison of heatmaps.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_downloads.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_downloads.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,150 @@ + + + + + + + + + + + +
+ +

The +filtered dataset: Allows you to download information on V D and J gene usage, +the junctions and the amino acid sequence of the sequences that passed the chosen +filter settings. Note: this file contains only 1 sequences of a replicate +sequence.

+ +

The +dataset used to calculate clonality score: Allows you to +download information on V D and J gene usage, the junctions and the amino acid +sequence of the sequences that passed the chosen filter settings. Note: this +file contains all the replicate sequences form the different input files.

+ +

The dataset used to generate the CDR3 +length frequency graph: Downloads a table with information used for the +length distribution of CDR3 plot.

+ +

The dataset used to generate the distribution +of V gene families graph: Downloads a table with information used to generate +the distribution of V gene families graph.

+ +

The dataset used to generate the +distribution of D gene families graph: Downloads a table with information used +to generate the distribution of D gene families graph.

+ +

The +dataset used to generate the relative frequency of V gene usage graph: +Downloads the data used to generate the relative frequency of V gene usage +graph. In addition information on the chromosomal order of the V genes can be +found.

+ +

The +dataset used to generate the relative frequency of D gene usage graph: +Downloads the data used to generate the relative frequency of D gene usage +graph. In addition information on the chromosomal order of the D genes can be +found.

+ +

The +dataset used to generate the relative frequency of J gene usage graph: Downloads +the data used to generate the relative frequency of J gene usage graph. In +addition information on the chromosomal order of the J genes can be found.

+ +

The +dataset used to generate the Amino Acid Composition in the CDR3 graph: +Downloads the frequency of the different amino acids in the CDR3 of all +filtered sequences. This data set is used for the generation of the Amino Acid +Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity +in included.

+ +

The +data used to generate the VD heatmap for donor name: +Downloads the data set used for the generation of the VD heatmap. For each +uploaded donor a separate download is generated.

+ +

The +data used to generate the VJ heatmap for donor name: +Downloads the data set used for the generation of the VJ heatmap. For each +uploaded donor a separate download is generated.

+ +

The +data used to generate the DJ heatmap for sample name: +Downloads the data set used for the generation of the DJ heatmap. For each +uploaded donor a separate download is generated.

+ +

A +frequency count of a clonotype: The frequency count of +a clonotype in the unfiltered data set. The clonotype defition used is defined +in the clonal type definition filter.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_gene_freq.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_gene_freq.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,106 @@ + + + + + + + + + + + +
+ +

This tab gives information on the +frequency of V, D and J gene usage.

+ +

Graphs

+ +

Distribution of V gene families

+ +

Bar graph showing the frequency +of V gene family usage in all uploaded donors.

+ +

Relative frequency of V gene +usage

+ +

Bar graph showing the frequency +of V genes in all uploaded donors. The order of the V genes on the x-axis can +be altered by altering the Order of +V(D)J genes in graphs filter on the main page of the Immune repertoire +pipeline.

+ +

Relative +frequency of D gene usage

+ +

Bar graph showing the frequency of D +genes in all uploaded donors. The order of the D genes on the x-axis can be +altered by altering the Order of +V(D)J genes in graphs filter on the main page of the Immune repertoire +pipeline.

+ +

Relative +frequency of J gene usage

+ +

Bar graph showing the frequency of J +genes in all uploaded donors. The order of the J genes on the x-axis can be +altered by altering the Order of +V(D)J genes in graphs filter on the main page of the Immune repertoire +pipeline.

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_heatmap.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_heatmap.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,57 @@ + + + + + + + + + + + +
+ +

In this tab +heatmaps are provided showing the frequency of different combinations V and D, +D and J and V and J genes according together. For each donor a subtab with all +three heatmaps is provided.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_junction.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_junction.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,94 @@ + + + + + + + + + + + +
+ +

Tables:

+ +

Productive +mean table

+ +

Reports for each +donor the number of productive sequences and the mean number of deletions, +N-nucleotides and P-nucleotides. For explanation about the different deletions +and N and P nucleotides see figure above.

+ +

Unproductive +mean table

+ +

Reports for each +donor the number of unproductive sequences and the mean number of deletions, +N-nucleotides and P-nucleotides. For explanation about the different deletions +and N and P nucleotides see figure above.

+ +

Productive +median table

+ +

Reports for each +donor the number of productive sequences and the median number of deletions, +N-nucleotides and P-nucleotides. For explanation about the different deletions +and N and P nucleotides see figure above.

+ +

Unproductive +median table

+ +

Reports for each +donor the number of unproductive sequences and the median number of deletions, +N-nucleotides and P-nucleotides. For explanation about the different deletions +and N and P nucleotides see figure above.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/naive_overview.htm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report_clonality/naive_overview.htm Wed Dec 21 11:53:03 2016 -0500 @@ -0,0 +1,65 @@ + + + + + + + + + + + +
+ +

Table showing the number and percentage of +(unique) productive and unproductive sequences per sample and per replicate.

+ +

 

+ +

The definition +of unique sequences is based on the clonal type definition filter setting +chosen.

+ +

 

+ +
+ + + + diff -r da95be204ebc -r 5d11c9139a55 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Wed Dec 21 05:57:31 2016 -0500 +++ b/report_clonality/r_wrapper.sh Wed Dec 21 11:53:03 2016 -0500 @@ -47,7 +47,10 @@ echo "$unproductive (${perc_unprod}%)" >> $2 echo "$unproductive_unique (${perc_unprod_un}%)" >> $2 done < $outputDir/productive_counting.txt -echo "" >> $2 +echo "
" >> $2 +echo "Table showing the number and percentage of (unique) productive and unproductive sequences per sample and per replicate.
" >> $2 +echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 +echo "" >> $2 echo "Report on:" >> $outputFile @@ -124,6 +127,9 @@ echo "<img src='DPlot.png'/>" >> $outputFile fi echo "<img src='JPlot.png'/>" >> $outputFile + +cat $dir/naive_gene_freq.htm >> $outputFile + echo "</div>" >> $outputFile echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile @@ -139,6 +145,8 @@ done < $outputDir/AAMedianBySample.csv echo "</table>" >> $outputFile +cat $dir/naive_cdr3_char.htm >> $outputFile + echo "</div>" >> $outputFile #Heatmaps @@ -157,8 +165,25 @@ echo "</tr></table></div>" >> $outputFile count=$((count+1)) done + +cat $dir/naive_heatmap.htm >> $outputFile + echo "</div></div>" >> $outputFile +echo "<div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile +for sample in $samples; do + echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile +done +echo "</table><div name='comparisonarea'>" >> $outputFile +echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile +echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile +echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile + +cat $dir/naive_compare.htm >> $outputFile + +echo "</div></div>" >> $outputFile + + #circos if [[ "$USECIRCOS" == "yes" ]]; then @@ -176,6 +201,9 @@ echo "<center></table></div>" >> $outputFile count=$((count+1)) done + + cat $dir/naive_circos.htm >> $outputFile + echo "</div></div>" >> $outputFile fi #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile @@ -239,6 +267,9 @@ echo "</table></div>" >> $outputFile fi done + + cat $dir/naive_clonality.htm >> $outputFile + echo "</div></div>" >> $outputFile fi @@ -249,66 +280,58 @@ echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile - echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median do echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile done < $outputDir/junctionAnalysisProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median do echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile done < $outputDir/junctionAnalysisUnProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median do echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile done < $outputDir/junctionAnalysisProd_median.csv echo "</tbody></table>" >> $outputFile - echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile + echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median do echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile done < $outputDir/junctionAnalysisUnProd_median.csv echo "</tbody></table>" >> $outputFile + cat $dir/naive_junction.htm >> $outputFile + echo "</div>" >> $outputFile fi -echo "<div class='tabbertab' title='Comparison'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile -for sample in $samples; do - echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile -done -echo "</table><div name='comparisonarea'>" >> $outputFile -echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile -echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile -echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile -echo "</div></div>" >> $outputFile - echo "<div class='tabbertab' title='Downloads'>" >> $outputFile echo "<table class='pure-table pure-table-striped'>" >> $outputFile echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $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 filtered dataset</td><td><a href='allUnique.txt'>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.txt'>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 distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile if [[ "$useD" == "true" ]] ; then - 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 distribution of D gene families graph</td><td><a href='DFFrequency.txt'>Download</a></td></tr>" >> $outputFile fi -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 relative frequency of V gene usage graph</td><td><a href='VFrequency.txt'>Download</a></td></tr>" >> $outputFile if [[ "$useD" == "true" ]] ; then - 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 relative frequency of D gene usage graph</td><td><a href='DFrequency.txt'>Download</a></td></tr>" >> $outputFile fi -echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile -echo "<tr><td>The dataset used to generate the AA composition graph</td><td><a href='AAComposition.csv'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href='JFrequency.txt'>Download</a></td></tr>" >> $outputFile +echo "<tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href='AAComposition.txt'>Download</a></td></tr>" >> $outputFile for sample in $samples; do if [[ "$useD" == "true" ]] ; then @@ -323,4 +346,7 @@ echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile echo "</table>" >> $outputFile + +cat $dir/naive_downloads.htm >> $outputFile + echo "</div></html>" >> $outputFile