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plot_log2_fpkm_dist = function (fpkm_files) {
num_files = length(fpkm_files);
data_list = list();
max_y = 0
xlim = c(0,0)
for (i in 1:num_files) {
file = fpkm_files[i]
data = read.table(file, header=F)
data = data[,6];
data = log2(data+1)
den = density(data);
data_list[[i]] = den
y = max(den$y);
if (y > max_y) {
max_y = y;
}
x = min(den$x)
if (x < xlim[1]) {
xlim[2] = x
}
x = max(den$x);
if (x > xlim[2]) {
xlim[2] = x
}
}
colors = rainbow(num_files);
for (i in 1:num_files) {
if (i == 1) {
plot(data_list[[1]], col=colors[1], xlim=xlim, ylim=c(0,max_y), xlab="log2(fpkm+1)")
}
else {
points(data_list[[i]], col=colors[i], type='l')
}
}
return;
}
plot_expressed_gene_counts = function(fpkm_file,
title="expressed transcript counts vs. min fpkm",
fpkm_range=seq(0,10,0.2),
total=0,
outfile="count_summary.txt") {
data = read.table(fpkm_file, header=T, row.names=1);
data = data[,5]
counts_expressed = c();
counts_not_expressed = c();
print_not_expressed_flag = 1;
if (total == 0) {
total = length(data);
print_not_expressed_flag = 0;
}
count_expressed = total;
for (i in fpkm_range) {
if (i > 0) {
count_expressed = sum(data>=i)
}
count_not_expressed = total - count_expressed;
counts_expressed[length(counts_expressed)+1] = count_expressed;
counts_not_expressed[length(counts_not_expressed)+1] = count_not_expressed;
}
orig_settings = par(mfrow=c(1,2))
plot(fpkm_range, counts_expressed, type='o', col='black', xlab="min(fpkm)",
main=title, ylab="count of transcripts", ylim=c(0,max(counts_expressed, counts_not_expressed)))
if (print_not_expressed_flag) {
points(fpkm_range, counts_not_expressed, type='o', col='blue')
legend('topright', c('expressed', 'not expressed'), col=c('black', 'blue'), pch=15);
}
else {
legend('bottomright', c('expressed transcripts'), col=c('black'), pch=15);
}
data_table = data.frame(fpkm_range=fpkm_range, expressed=counts_expressed, not_expressed=counts_not_expressed);
write.table(data_table, file=outfile, quote=F, sep='\t', row.names=F);
## make density plot for non-zero FPKM values
data = data[data>0]
plot(density(log2(data)), xlab="log2(fpkm)")
par(orig_settings)
}
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