| Previous changeset 37:f37e072affc0 (2017-04-19) Next changeset 39:bad6a9a53ae7 (2017-04-24) |
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modified:
report_clonality/RScript.r report_clonality/r_wrapper.sh |
| b |
| diff -r f37e072affc0 -r b6936fb52ab9 report_clonality/RScript.r --- a/report_clonality/RScript.r Wed Apr 19 08:05:01 2017 -0400 +++ b/report_clonality/RScript.r Wed Apr 19 10:21:01 2017 -0400 |
| [ |
| b'@@ -768,7 +768,7 @@\n Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)),\n Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n- Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length, na.rm=T)))),\n+ Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisProd_mean_wD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n@@ -787,7 +787,7 @@\n \t\t\t\t\t\t\t\t\t\t\t Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n \t\t\t\t\t\t\t\t\t\t\t Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)),\n \t\t\t\t\t\t\t\t\t\t\t Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n-\t\t\t\t\t\t\t\t\t\t\t Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length, na.rm=T)))),\n+\t\t\t\t\t\t\t\t\t\t\t Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisProd_median_wD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n@@ -806,7 +806,7 @@\n Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n Total.N=mean(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)),\n Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n- Median.CDR3.l=as.double(as.numeric(median(.SD$CDR3.Length, na.rm=T)))),\n+ Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisUnProd_mean_wD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n@@ -825,7 +825,7 @@\n Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n Total.N=num_median(rowSums(.SD[,c("N.REGION.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "N3.REGION.nt.nb", "N4.REGION.nt.nb"), with=F], na.rm=T)),\n Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n- Median.CDR3.l=as.double(as.numeric(median(.SD$CDR3.Length, na.rm=T)))),\n+ Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n \t\t\t\t\t\t\t\t\t\t\t\t\t\t\tby=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,s'..b' by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisProd_mean_nD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n@@ -855,13 +855,11 @@\n \t\t\t\t\t\t\t\t\t\t\t Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n \t\t\t\t\t\t\t\t\t\t\t Total.N=num_median(.SD$N.REGION.nt.nb, na.rm=T),\n \t\t\t\t\t\t\t\t\t\t\t Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n-\t\t\t\t\t\t\t\t\t\t\t Median.CDR3.l=as.double(as.numeric(median(.SD$CDR3.Length, na.rm=T)))),\n+\t\t\t\t\t\t\t\t\t\t\t Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisProd_median_nD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n \n- print(paste("mean N:", mean(UNPROD.no.D$N.REGION.nt.nb, na.rm=T)))\n- \n newData = data.frame(data.table(UNPROD.no.D)[,list(unique=.N, \n VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),\n P1=mean(.SD$P3V.nt.nb, na.rm=T),\n@@ -871,12 +869,11 @@\n Total.Del=mean(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n Total.N=mean(.SD$N.REGION.nt.nb, na.rm=T),\n Total.P=mean(rowSums(.SD[,c("P3V.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n- Median.CDR3.l=as.double(as.numeric(median(.SD$CDR3.Length, na.rm=T)))),\n+ Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n by=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisUnProd_mean_nD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n \n- print(paste("median N:", num_median(UNPROD.no.D$N.REGION.nt.nb, na.rm=T)))\n \n newData = data.frame(data.table(UNPROD.no.D)[,list(unique=.N, \n VH.DEL=num_median(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),\n@@ -887,7 +884,7 @@\n Total.Del=num_median(rowSums(.SD[,c("X3V.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb"), with=F], na.rm=T)),\n Total.N=num_median(.SD$N.REGION.nt.nb, na.rm=T),\n Total.P=num_median(rowSums(.SD[,c("P3V.nt.nb", "P5J.nt.nb"), with=F], na.rm=T)),\n- Median.CDR3.l=as.double(as.numeric(median(.SD$CDR3.Length, na.rm=T)))),\n+ Median.CDR3.l=as.double(median(as.numeric(.SD$CDR3.Length), na.rm=T))),\n \t\t\t\t\t\t\t\t\t\t\t\t\t\t\tby=c("Sample")])\n newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)\n write.table(newData, "junctionAnalysisUnProd_median_nD.txt" , sep="\\t",quote=F,na="-",row.names=F,col.names=F)\n@@ -927,7 +924,6 @@\n \n ggsave("DReadingFrame.pdf", D.REGION.reading.frame)\n \n-\n # ---------------------- AA composition in CDR3 ----------------------\n \n AACDR3 = PRODF[,c("Sample", "CDR3.Seq")]\n@@ -977,6 +973,7 @@\n \n #generate the "Sequences that are present in more than one replicate" dataset\n clonaltype.in.replicates = inputdata\n+clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),]\n clonaltype.in.replicates = na.omit(clonaltype.in.replicates)\n clonaltype = unlist(strsplit(clonaltype, ","))\n \n@@ -1023,5 +1020,3 @@\n \n \n \n-\n-\n' |
| b |
| diff -r f37e072affc0 -r b6936fb52ab9 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Wed Apr 19 08:05:01 2017 -0400 +++ b/report_clonality/r_wrapper.sh Wed Apr 19 10:21:01 2017 -0400 |
| b |
| b'@@ -273,28 +273,28 @@\n \techo "<img src=\'IGH_junctie_analyse.png\' />" >> $outputFile\n \t\n \techo "<center><p style=\'font-size: 20;\'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive mean</caption><thead><tr><th>Donor</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive mean</caption><thead><tr><th>Donor</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$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\n \tdone < $outputDir/junctionAnalysisProd_mean_wD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive mean</caption><thead><tr><th>Donor</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive mean</caption><thead><tr><th>Donor</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$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>-</td></tr>" >> $outputFile\n \tdone < $outputDir/junctionAnalysisUnProd_mean_wD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive median</caption><thead><tr><th>Donor</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive median</caption><thead><tr><th>Donor</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$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\n \tdone < $outputDir/junctionAnalysisProd_median_wD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'>'..b'able pure-table-striped\' id=\'junction_table\'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile\n \tdone < $outputDir/junctionAnalysisProd_mean_nD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile\n \tdone < $outputDir/junctionAnalysisUnProd_mean_nD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile\n \tdone < $outputDir/junctionAnalysisProd_median_nD.txt\n \techo "</tbody></table>" >> $outputFile\n \t\n-\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</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\n+\techo "<table class=\'pure-table pure-table-striped\' id=\'junction_table\'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile\n \twhile read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median\n \tdo\n \t\techo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile\n' |