Cluster methods used by VIRTUS and heatmap issue

[patrick-douglas]

Dear yyoshiaki,

I`m having a issue during a VIRTUS run, I have two cases:

1° case: I have 14 samples divided in 3 groups,
Group 01: 4 samples
Group 02: 06 samples
Group 03: 04 samples

The final heatmap show only 11 samples

2° case: I have 12 samples divided in 3 group,
Group 01: 04 samples
Group 02: 04 samples
Group 03: 04 samples

The final heatmap shows only 09 samples

How can I fix the heatmap to show all samples?

I also would like to know which clustering method is used by VIRTUS, I've tried some (e.g. Complete linkage, average linkage, etc.), but none reproduced the same heatmap generated by VIRTUS, even using only samples in the original VIRTUS heatmap.

Another question is, should I use the summary.csv for heatmap construction?

Thank you in advance

Patrick.

[yyoshiaki]

Hi Patrick,

Sorry, as I cannot reproduce the problem, I have no idea about it.
Can you modify VIRTUS_wrapper.py or, by scratch, make figures?
Using summary.csv is a simple solution.