# load the data and the dictionary
patients <- levels(as.factor(dict$patient))
path <- '/home/ahopkins/Documents/emj/ImmunoseqResults/adjuvant_study/plots/'
for(a in seq_along(patients)){
# make data subsets
w <- which(dict$patient==patients[a])
response <- as.character(dict$response[which(dict$patient==patients[a] & dict$type=='PRE')])
tds <- ds[ ,w]
tdict <- dict[w, ]
# get pre and post
pre <- tds[ ,which(tdict$type=='PRE')]
post <- tds[ ,which(tdict$type=='POST')]
x <- (pre!=0 | post!=0)
pre <- pre[x]
post <- post[x]
# calculate overlap
ol <- overlap(pre,post)
# plot
dir.create(paste0(path,'Corr/'))
pdf(paste0(path,'Corr/',patients[a],'_corr.pdf'),
width=8.5,height=8,
title=paste('Correlation Plot for',patients[a]))
par(oma=c(1,4,1,1))
r <- range(pre,post)[2]*1.05
plot(post,pre,pch=".",asp=1,
main=paste0(patients[a],'(',response,')'),
xlim=c(1,r),ylim=c(1,r),
xlab='Post',
ylab='Pre',
log='xy',
cex.lab=1.5,
cex.main=2)
grid()
text(r/100,r,paste0("o=",round(ol,4)),cex=1.5)
dev.off()
}
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