summary - PCA done for group of samples not for samples, time points

[mmaslon]

I am trying to run PCA analysis with alleyoop summary. I have several samples, e.g. LKO rep1 0', LKO rep2 0' ..... MUT1 rep1 0', MUT rep2 0' .... MUT2 rep1 0', MUT2 rep2 0',
When I run the summary, I get the PCA plots for LKO vs MUT1 vs MUT2, rather than individual samples (e..g. I would rather see how same time points look for different conditions). I am not sure what I am doing wrong,
my code is"

alleyoop summary -o $output_dir/summary -t $tcount $bam/*.bam

head of tcount file looks like this:

#slamdunk v0.4.3	3	sample info:	LKO	8	rep3	120

Can you please suggest what could be going wrong? I think this starts with the sample info, the info on replica and time poiint is somehow not taken into account.

Thanks