Diploid and aneuploid reversed

[LeaLe88]

Good afternoon,

I have ran copykat on one tumour sample. I was expecting to see aneuploid in the epithelial/tumour cluster and diploid in the remaining cluster. However, I got the opposite result. Please find the clustering below:

I do receive the error "low confidence in classification" as described in #18.

I followed the suggestions in issue 18 and limited my analysis to epithelial cells only.
However again I get the error "low confidence in classification" and I see a mix of diploid and aneuploid in the epithelial cells:

Do you know what else I could do to obtain a correct annotation of my clusters?

Thank you very much!