Nothing
## Julia Bischof
## 10-09-2015
plotTrueDiversity<-function(trueDiversity.tab=NULL, mean.plot=T, color="black", PDF=NULL){
if(length(trueDiversity.tab)==0){
stop("--> True diversity tab is missing or empty")
}
if(mean.plot==T){
if(length(PDF)>0){
pdf(paste(PDF,"_True-diversity_q",as.numeric(trueDiversity.tab$True_diversity_order),".pdf",sep=""),
width=9,height=7, pointsize =16)
}
par(mfrow=c(1,1),mar=c(5,5,2,2), oma=c(1,1,4,1))
plot(1,1,col="white",xlab="CDR3 length [AA]", ylab="Mean diversity", xlim=c(1,length(trueDiversity.tab$True_diversity)+2),
ylim=c(0, max(unlist(trueDiversity.tab),na.rm=T)))
m<-vector()
s<-vector()
for(i in 1:length(trueDiversity.tab$True_diversity)){
m<-c(m, mean(as.numeric(trueDiversity.tab$True_diversity[[i]]), na.rm=T))
s<-c(s, sd(as.numeric(trueDiversity.tab$True_diversity[[i]]), na.rm=T))
}
points(x = as.numeric(apply(data.frame(names(trueDiversity.tab$True_diversity)),1,function(x){strsplit(x, split="= ")[[1]][2]})), m, pch=16, col=color, cex=1.3)
lines(x = as.numeric(apply(data.frame(names(trueDiversity.tab$True_diversity)),1,function(x){strsplit(x, split="= ")[[1]][2]})), m, lwd=2, col=color)
CI.up = as.numeric(m)+as.numeric(s)
CI.dn = as.numeric(m)-as.numeric(s)
options(warn=-1)
arrows(as.numeric(apply(data.frame(names(trueDiversity.tab$True_diversity)),1,function(x){strsplit(x, split="= ")[[1]][2]})),CI.dn,
as.numeric(apply(data.frame(names(trueDiversity.tab$True_diversity)),1,function(x){strsplit(x, split="= ")[[1]][2]})),CI.up,code=3,length=0.05,angle=90,col=color)
options(warn=0)
}else{
if(length(PDF)>0){
pdf(file = paste(PDF,"_True-diversity_q",trueDiversity.tab$True_diversity_order,".pdf",sep=""),
width = ceiling(sqrt(length(trueDiversity.tab$True_diversity)))*5.5,
height = floor(sqrt(length(trueDiversity.tab$True_diversity)))*6.6,
pointsize = if(sqrt(length(trueDiversity.tab$True_diversity)+1)*4<32){32}else{sqrt(length(trueDiversity.tab$True_diversity)+1)*4},onefile = F)
}
par(mfrow=if(ceiling(sqrt(length(trueDiversity.tab$True_diversity)))*floor(sqrt(length(trueDiversity.tab$True_diversity)))>length(trueDiversity.tab$True_diversity)){c(ceiling(sqrt(length(trueDiversity.tab$True_diversity))),floor(sqrt(length(trueDiversity.tab$True_diversity))))}else{c(ceiling(sqrt(length(trueDiversity.tab$True_diversity))),ceiling(sqrt(length(trueDiversity.tab$True_diversity))))},
mar=c(5,5,5,3),oma=c(1,1,5,1))
for(i in 1:length(trueDiversity.tab$True_diversity)){
plot(as.numeric(trueDiversity.tab$True_diversity[[i]][1,]),col=color,type="b", cex=0.8,
ylab=if(trueDiversity.tab$True_diversity_order==0){"Richness"}else{"Diversity"},
xlab="Position",axes=F,ylim=c(0,max(unlist(trueDiversity.tab$True_diversity),na.rm=T)+5),
main=names(trueDiversity.tab$True_diversity)[i])
if(ncol(trueDiversity.tab$True_diversity[[i]])>11){
axis(1,at=c(1,round(ncol(trueDiversity.tab$True_diversity[[i]])*seq(0.25,1,0.25),0)),c(1,round(ncol(trueDiversity.tab$True_diversity[[i]])*seq(0.25,1,0.25),0)))
}else if(ncol(trueDiversity.tab$True_diversity[[i]])>6 && ncol(trueDiversity.tab$True_diversity[[i]])<=11){
axis(1,at=seq(1,ncol(trueDiversity.tab$True_diversity[[i]])+1, 2), seq(1,ncol(trueDiversity.tab$True_diversity[[i]])+1, 2))
}else{
axis(1,at=1:ncol(trueDiversity.tab$True_diversity[[i]]), 1:ncol(trueDiversity.tab$True_diversity[[i]]))
}
axis(2,at=seq(0,max(unlist(trueDiversity.tab$True_diversity),na.rm=T)+5,5),seq(0,max(unlist(trueDiversity.tab$True_diversity),na.rm=T)+5,5))
}
}
title(paste("True diversity, order ",as.numeric(trueDiversity.tab$True_diversity_order),sep=""),outer=T, cex.main=2)
if(length(PDF)>0){
dev.off()
}
}
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