library(immunoSeqR)
load('~/Documents/emj/ImmunoseqResults/sampleExport.2014-07-31_10-10-24/ds_agg_reorder.Rda')
load('~/Documents/emj/ImmunoseqResults/sampleExport.2014-07-31_10-10-24/dict_reorder.Rda')
ds <- ds_agg_reorder
dict <- dict_reorder
byN=10
scans <- list()
for(a in seq(length(levels(dict$patient)))){
name <- levels(dict$patient)[a]
resp <- as.character(dict$response[which(dict$patient==name)][1])
samples <- c(which(dict$patient==name & dict$type=='Pre'),
which(dict$patient==name & dict$type=='Post')
)
# swap to rank by Pre or Post
tmp <- olScan(ds[,samples[1]],ds[,samples[2]],byN=byN)
scans[[name]] <- tmp
#save(tmp,file=paste0('~/Documents/emj/ImmunoseqResults/olscan/',name,'_by_',byN,'.Rda'))
}
save(scans,file=paste0('~/Documents/emj/ImmunoseqResults/olscan/all_by_',byN,'_Ranked_by_Post.Rda'))
#make plotting stuff
biggest <- max(unlist(lapply(scans,length)))
pdf(file=paste0('~/Documents/emj/ImmunoseqResults/olscan/olscan_by_',byN,'_Ranked_by_Post_zoom.pdf'),width=6,height=6)
plot(NA,
ylim=c(0,1),
xlim=c(1,1000),#1.02*biggest),
xlab=paste0('# of clones (x',byN,')'),
ylab='Overlap',
main='Overlap of top X clones')
for(a in seq(length(scans))){
resp <- as.character(dict$response[which(dict$patient==names(scans)[a])][1])
if(resp=='R'){color<-'blue'}else{color='red'}
points(seq(length(scans[[a]])),scans[[a]],col=color,pch='.')
text(length(scans[[a]]),min(scans[[a]]),paste(names(scans)[a]),pos=4,cex=0.6,offset=-0.02)
}
legend('topright',legend=c('R','NR'),col=c('blue','red'),pch=19,bg='white')
dev.off()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.