Nothing
## Julia Bischof
## 2016-02-24
plotSequencesMutationBase<-function(mutationBaseTab=NULL, plotEnvironment = FALSE, plotMutation = TRUE,
colHeatmap = c("white","darkblue"),title=NULL, PDF=NULL){
if(length(mutationBaseTab)==0){
stop("--> Output of sequences.mutation.base() is missing")
}
if(plotEnvironment == T){
if(is.list(mutationBaseTab)==T){
tab1<-mutationBaseTab$Environment
}else{
tab1<-mutationBaseTab
}
if(length(PDF)>0){
pdf(paste(PDF,"_Base-mutation_environment.pdf",sep=""), width = 7, height=7, pointsize = 10)
}
par(mfrow=c(2,2),mar=c(5,5,4,2),oma=c(2,2,4,2))
for(i in c("a_to","c_to","g_to","t_to")){
barplot(as.matrix(tab1[grep(i, rownames(tab1)),]), col=c("darkgreen","darkred","darkgray","darkblue"), yaxt="n", ylim=c(0,1), xlim=c(0,10),
names.arg = c("-3","-2","-1","0","+1","+2","+3"), xlab="Position", ylab="Percentage", main=paste(strsplit(i,split="_")[[1]][1]," -> n",sep=""))
axis(2,at = seq(0,1,0.25), seq(0,100,25))
legend("right", legend = c("t", "g","c","a"), col=c("darkblue", "darkgray","darkred","darkgreen"), y.intersp = 1.2, cex=1.1, pt.cex=2, pch=15)
}
title(title, outer=T, cex=1.8)
if(length(PDF)>0){
dev.off()
}
}
if(plotMutation==T){
if(is.list(mutationBaseTab)==T){
tab2<-mutationBaseTab$Mutated_position
}else{
tab2<-mutationBaseTab
}
if(length(PDF)>0){
pdf(paste(PDF,"_Base-mutation_mutated-position.pdf",sep=""), width = 9, height=7, pointsize = 10)
}
par(mfrow=c(1,1),oma=c(3,1,1,3), las=1)
heatmap.2(as.matrix(tab2),col=colorRampPalette(colHeatmap), Rowv=F,Colv=F,key=T,density.info="none", labRow = gsub("_"," ",rownames(tab2)), labCol = gsub("_"," ",colnames(tab2)),
trace="none",cexCol=1.5,cexRow=1.5,dendrogram="none", keysize = 1.5,key.xlab="proportion")
title(title, outer=T, cex=1.8)
if(length(PDF)>0){
dev.off()
}
}
}
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