Nothing
reliabilityCheckLibrary <- function(seedlib.file, extlib.file)
{
dlib = list()
dlib[[1]] = readLibFile(seedlib.file)
dlib[[2]] = read.delim(extlib.file, sep='\t', stringsAsFactors=FALSE)
# pep.col = c('Q1','stripped_sequence','modification_sequence', 'uniprot_id')
lib.labels = c('seed.library', 'extended.library')
lib.stats = matrix(NA, nrow=length(dlib), ncol=2)
rownames(lib.stats) = lib.labels
colnames(lib.stats) = c('proteins','peptides')
for( ii in 1:length(dlib)) {
x = dlib[[ii]]
lib.stats[ii,] = c(length(unique(x$uniprot_id)), length(unique(x$modification_sequence)) )
}
# barplots
png('plots_of_library_info.png', 2500, 3500, res=300)
sl = ceiling(max(lib.stats[,1])/1000)/ceiling(max(lib.stats[,2])/1000)
pepnum.scaled = lib.stats[,2]*sl
ymax = 1.1*max(c(lib.stats[,1], pepnum.scaled))
bp1 = barplot(lib.stats[,1], space=0.5, names.arg=lib.labels, ylim=c(0, ymax),
ylab='Number of proteins', axes=FALSE, col=gray(0.8), main='Libraries')
at1 = axis(side=2)
points(bp1, lib.stats[,2]*sl, type='b', lwd=3, col=gray(0.4) )
at2 = round(at1/(sl*1000))*1000
axis(side=4, at = at1, labels=at2)
mtext('Number of peptides', side=4, line=3)
par(xpd=TRUE)
legend(bp1[1,1], ceiling(1.05*ymax) , bty='n', fill=gray(0.8), legend='protein')
legend(bp1[2,1], ceiling(1.05*ymax), bty='n', col=gray(0.4), lty=1, legend='peptide', lwd=2)
dev.off()
lib.stats = rbind(lib.stats, c(coverage(dlib[[1]]$uniprot_id, dlib[[2]]$uniprot_id),
coverage(dlib[[1]]$modification_sequence, dlib[[2]]$modification_sequence) ) )
rownames(lib.stats)[3] = 'coverage.perc'
write.csv(lib.stats, 'table_library_coverage.csv')
lib.stats
}
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