Hi, guys. First of all, I appreciate your effort.

I have one question about output file.

Whenever I got png file for result in each step, I can't see subcluster information in figure. (except for subcluster.png)

I really hope to get final result with subcluster and observation group at once.

I'm curious it's because of package version. Or do I need to set the option when I run the code?

So I'll attach my code, package version, and result figure.

Please check it.

Thank you!

code

infercnv_obj = infercnv::run(infercnv_obj , cutoff=0.1, out_dir=".", cluster_by_groups=T, denoise=TRUE, HMM=TRUE, leiden_resolution=0.002, tumor_subcluster_pval=0.05)

package version

infercnv 1.14.2 ver

result picture

final figure
subcluster figure

broadinstitute / infercnv

Output file issue #565

code

package version

result picture