Mercurial > repos > davidvanzessen > shm_csr
changeset 23:81453585dfc3 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 01 Dec 2016 09:32:06 -0500 |
| parents | 0bea8c187a90 |
| children | 9955b23db68c |
| files | aa_histogram.r pattern_plots.r shm_csr.r wrapper.sh |
| diffstat | 4 files changed, 141 insertions(+), 88 deletions(-) [+] |
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--- a/aa_histogram.r Mon Nov 28 10:27:22 2016 -0500 +++ b/aa_histogram.r Thu Dec 01 09:32:06 2016 -0500 @@ -15,50 +15,49 @@ absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="") for(gene in genes){ + if(gene == ""){ + mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),] + absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),] + } else { + mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),] + absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),] + } + print(paste("nrow", gene, nrow(absent.aa.by.id.gene))) + if(nrow(mutations.by.id.gene) == 0){ + next + } - if(gene == ""){ - mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),] - absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),] - } else { - mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),] - absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),] - } - print(paste("nrow", gene, nrow(absent.aa.by.id.gene))) - if(nrow(mutations.by.id.gene) == 0){ - next - } - - mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)]) - aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)]) + mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)]) + aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)]) - dat_freq = mutations.at.position / aa.at.position - dat_freq[is.na(dat_freq)] = 0 - dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq) + dat_freq = mutations.at.position / aa.at.position + dat_freq[is.na(dat_freq)] = 0 + dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq) - print("---------------- plot ----------------") + print("---------------- plot ----------------") - m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1), text = element_text(size=13, colour="black")) - m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i) - m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1") - m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1") - m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2") - m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2") - m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3") - m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) - m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) - m = m + scale_colour_manual(values=c("black")) + m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1), text = element_text(size=13, colour="black")) + m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i) + m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1") + m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1") + m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2") + m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2") + m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3") + m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) + m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank()) + #m = m + scale_colour_manual(values=c("black")) - print("---------------- write/print ----------------") + print("---------------- write/print ----------------") - dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) + dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) - write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) - write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) - write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) - write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) - - png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) - print(m) - dev.off() + write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + + png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) + print(m) + dev.off() }
--- a/pattern_plots.r Mon Nov 28 10:27:22 2016 -0500 +++ b/pattern_plots.r Thu Dec 01 09:32:06 2016 -0500 @@ -18,6 +18,8 @@ plot3.png = paste(plot3.path, ".png", sep="") plot3.txt = paste(plot3.path, ".txt", sep="") +clean.output = args[5] + dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T, row.names=1) @@ -28,6 +30,11 @@ names(dat) = new.names +clean.dat = dat +clean.dat = clean.dat[,c(paste(rep(classes, each=3), xyz, sep="."), paste("all", xyz, sep="."), paste("un", xyz, sep="."))] + +write.table(clean.dat, clean.output, quote=F, sep="\t", na="", row.names=T, col.names=NA) + dat["RGYW.WRCY",] = colSums(dat[c(13,14),], na.rm=T) dat["TW.WA",] = colSums(dat[c(15,16),], na.rm=T) @@ -51,26 +58,24 @@ print(p) dev.off() -data2 = dat[5:8,] - -data2["sum",] = colSums(data2, na.rm=T) +data2 = dat[c(1, 5:8),] data2 = data2[,names(data2)[grepl("\\.x", names(data2))]] names(data2) = gsub(".x", "", names(data2)) -data2["A/T",] = round(colSums(data2[3:4,]) / data2["sum",] * 100, 1) -data2["A/T",is.nan(unlist(data2["A/T",]))] = 0 +data2["A/T",] = dat["Targeting of A T (%)",names(dat)[grepl("\\.z", names(dat))]] -data2["G/C transversions",] = round(data2[2,] / data2["sum",] * 100, 1) -data2["G/C transitions",] = round(data2[1,] / data2["sum",] * 100, 1) +data2["G/C transitions",] = round(data2["Transitions at G C (%)",] / data2["Number of Mutations (%)",] * 100, 1) +data2["mutation.at.gc",] = dat["Transitions at G C (%)",names(dat)[grepl("\\.y", names(dat))]] +data2["G/C transversions",] = round((data2["mutation.at.gc",] - data2["Transitions at G C (%)",]) / data2["Number of Mutations (%)",] * 100, 1) data2["G/C transversions",is.nan(unlist(data2["G/C transversions",]))] = 0 data2["G/C transversions",is.infinite(unlist(data2["G/C transversions",]))] = 0 data2["G/C transitions",is.nan(unlist(data2["G/C transitions",]))] = 0 data2["G/C transitions",is.infinite(unlist(data2["G/C transitions",]))] = 0 -data2 = melt(t(data2[6:8,])) +data2 = melt(t(data2[c("A/T","G/C transitions","G/C transversions"),])) names(data2) = c("Class", "Type", "value") @@ -92,11 +97,11 @@ data3[is.na(data3)] = 0 #data3[is.infinite(data3)] = 0 -data3["G/C transitions",] = round(data3[1,] / (data3[5,] + data3[7,]) * 100, 1) +data3["G/C transitions",] = round(data3["Transitions at G C (%)",] / (data3["C",] + data3["G",]) * 100, 1) -data3["G/C transversions",] = round(data3[2,] / (data3[5,] + data3[7,]) * 100, 1) +data3["G/C transversions",] = round((data3["Targeting of G C (%)",] - data3["Transitions at G C (%)",]) / (data3["C",] + data3["G",]) * 100, 1) -data3["A/T",] = round(data3[3,] / (data3[4,] + data3[6,]) * 100, 1) +data3["A/T",] = round(data3["Targeting of A T (%)",] / (data3["A",] + data3["T",]) * 100, 1) data3["G/C transitions",is.nan(unlist(data3["G/C transitions",]))] = 0 data3["G/C transitions",is.infinite(unlist(data3["G/C transitions",]))] = 0
--- a/shm_csr.r Mon Nov 28 10:27:22 2016 -0500 +++ b/shm_csr.r Thu Dec 01 09:32:06 2016 -0500 @@ -15,7 +15,7 @@ if(length(dat$Sequence.ID) == 0){ setwd(outputdir) result = data.frame(x = rep(0, 5), y = rep(0, 5), z = rep(NA, 5)) - row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)") + row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)") write.table(x=result, file="mutations.txt", sep=",",quote=F,row.names=T,col.names=F) transitionTable = data.frame(A=rep(0, 4),C=rep(0, 4),G=rep(0, 4),T=rep(0, 4)) row.names(transitionTable) = c("A", "C", "G", "T") @@ -296,9 +296,9 @@ transition2 = merge(transition2, base.order, by.x="variable", by.y="base") transition2[is.na(transition2$value),]$value = 0 - + if(any(transition2$value != 0)){ #having rows of data but a transition table filled with 0 is bad - print("Plotting stacked transition") + print("Plotting heatmap and transition") png(filename=paste("transitions_stacked_", name, ".png", sep="")) p = ggplot(transition2, aes(factor(reorder(id, order.x)), y=value, fill=factor(reorder(variable, order.y)))) + geom_bar(position="fill", stat="identity", colour="black") #stacked bar p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) @@ -306,16 +306,13 @@ #p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black")) print(p) dev.off() - - print("Plotting heatmap transition") - png(filename=paste("transitions_heatmap_", name, ".png", sep="")) p = ggplot(transition2, aes(factor(reorder(id, order.x)), factor(reorder(variable, order.y)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) print(p) dev.off() } else { - print("No data to plot") + #print("No data to plot") } } @@ -338,22 +335,23 @@ func = funcs[[i]] fname = fnames[[i]] + print(paste("Creating table for", fname)) + rows = 9 if(fname == "sum"){ rows = 11 } matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=rows) for(i in 1:length(genes)){ - print(paste("Creating table for", fname, genes[i])) matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i]) } matrx = calculate_result(i + 1, ".*", dat[!grepl("unmatched", dat$best_match),], matrx, func, fname, name="all") result = data.frame(matrx) if(fname == "sum"){ - row.names(result) = c("Number of Mutations (%)", "Transitions (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR") + row.names(result) = c("Number of Mutations (%)", "Transitions (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR") } else { - row.names(result) = c("Number of Mutations (%)", "Transitions (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)") + row.names(result) = c("Number of Mutations (%)", "Transitions (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)") } write.table(x=result, file=paste("mutations_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=F) } @@ -368,7 +366,7 @@ new.table[,1] = as.character(new.table[,1]) new.table[2,1] = "Median of Number of Mutations (%)" -#sum.table = sum.table[c("Number of Mutations (%)", "Median of Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR"),] +#sum.table = sum.table[c("Number of Mutations (%)", "Median of Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of G C (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR"),] write.table(x=new.table, file="mutations_sum.txt", sep=",",quote=F,row.names=F,col.names=F) @@ -467,7 +465,9 @@ frequency_bins_data = data.frame(data.table(dat)[, list(frequency_count=.N), by=c("best_match", "best_match_class", "frequency_bins")]) -frequency_bins_data = merge(frequency_bins_data, frequency_bins_sum, by="best_match_class") +frequency_bins_sum = data.frame(data.table(dat)[, list(class_sum=sum(.N)), by=c("best_match")]) + +frequency_bins_data = merge(frequency_bins_data, frequency_bins_sum, by="best_match") frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2)
--- a/wrapper.sh Mon Nov 28 10:27:22 2016 -0500 +++ b/wrapper.sh Thu Dec 01 09:32:06 2016 -0500 @@ -230,7 +230,7 @@ echo "---------------- main tables ----------------<br />" >> $log echo "<div class='tabber'>" >> $output -echo "<div class='tabbertab' title='SHM Overview'>" >> $output +echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output for func in ${funcs[@]} do @@ -243,7 +243,7 @@ echo "---------------- pattern_plots.r ----------------" echo "---------------- pattern_plots.r ----------------<br />" >> $log - Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1 + Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1 echo "<table class='pure-table pure-table-striped'>" >> $output echo "<thead><tr><th>info</th>" >> $output @@ -301,7 +301,7 @@ echo "---------------- images ----------------" echo "---------------- images ----------------<br />" >> $log -echo "<div class='tabbertab' title='SHM Frequency'>" >> $output +echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output if [ -a $outdir/scatter.png ] then @@ -314,7 +314,7 @@ echo "</div>" >> $output #SHM frequency tab end -echo "<div class='tabbertab' title='Transition tables'>" >> $output +echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output echo "<table border='0'>" >> $output @@ -322,8 +322,21 @@ do echo "<tr>" >> $output echo "<td><h1>${gene}</h1></td>" >> $output - echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output - echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output + + if [ -e $outdir/transitions_heatmap_${gene}.png ] + then + echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output + else + echo "<td></td>" >> $output + fi + + if [ -e $outdir/transitions_stacked_${gene}.png ] + then + echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output + else + echo "<td></td>" >> $output + fi + echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output first="true" @@ -367,30 +380,66 @@ echo "<div class='tabbertab' title='Antigen Selection'>" >> $output -if [ -a $outdir/aa_histogram.png ] +if [ -e $outdir/aa_histogram.png ] then echo "<img src='aa_histogram.png'/><br />" >> $output +fi + +if [ -e $outdir/aa_histogram_IGA.png ] +then echo "<img src='aa_histogram_IGA.png'/><br />" >> $output +fi + +if [ -e $outdir/aa_histogram_IGG.png ] +then echo "<img src='aa_histogram_IGG.png'/><br />" >> $output +fi + +if [ -e $outdir/aa_histogram_IGM.png ] +then echo "<img src='aa_histogram_IGM.png'/><br />" >> $output +fi + +if [ -e $outdir/aa_histogram_IGE.png ] +then echo "<img src='aa_histogram_IGE.png'/><br />" >> $output fi -echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output -echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output -echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output -echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output -echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output + +if [ -e $outdir/baseline.png ] +then + echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output +fi + +if [ -e $outdir/baseline_IGA.png ] +then + echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output +fi + +if [ -e $outdir/baseline_IGG.png ] +then + echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output +fi + +if [ -e $outdir/baseline_IGM.png ] +then + echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output +fi + +if [ -e $outdir/baseline_IGE.png ] +then + echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output +fi echo "</div>" >> $output #antigen selection tab end echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab -if [ -a $outdir/IGA.png ] +if [ -e $outdir/IGA.png ] then echo "<img src='IGA.png'/><br />" >> $output fi -if [ -a $outdir/IGG.png ] +if [ -e $outdir/IGG.png ] then echo "<img src='IGG.png'/><br />" >> $output fi @@ -492,7 +541,7 @@ clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output echo "</div>" >> $output - echo "<div class='tabbertab' title='Overview'>" >> $output + echo "<div class='tabbertab' title='Overlap'>" >> $output cat "$outdir/sequence_overview/index.html" >> $output echo "</div>" >> $output @@ -512,7 +561,7 @@ echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output -echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output @@ -526,17 +575,17 @@ echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output -echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transition_all_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transition_IGA_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transition_IGG_sum.txt' download='transition_IGG_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transition_IGE_sum.txt' download='transition_IGE_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output