CNVs in the reference cells

[NaCo-Pt]

first thank you for this amazing tool. Second, I have very basic knoledge of coding so bear with me

I have used 2 cell types as references, CAFs and immune cells. Wihtin immune cells I can clearly see in the HM some cells with a CNV profile resembilg the tumor cells (observations bellow).
Does this mena I have some cells that were wrongly clustered with immune cells and could actually be tumor cells, or some doublets inside my immune cell cluster?
How can I identify which cells are those so when I go back to my seurat object I can isolate those cells and maybe exclude them from the analysis?

Another question, I have some cluster with a very reduced cell number and I cant visualize it well, like tje epithelial_cells. How cna I partioned my inferCNV heatmap to see just some clusters on the observation cells?

kind regards

[kiwipeel]

You can use some tumor related markers to isolate those cells among reference cells by subsetting based on the umi counts.