Numbat assigns clone coloring in Panel.png not uniquely

[Mashuaiii]

Hi @teng-gao ,

Thanks for building this tool, it's pretty cool!

The issue I'm facing is that the clones are not converging into single colors on my Y-axis despite being assigned as "subclones". Is this an issue or does that represent a degree of uncertainty with respect to the assignment? I noticed that the figures in the Numbat paper have clean separations of subclones so I wanted to check if what I am seeing is expected or not? Is there a way to set this so that the colors appear more continuous?

Any advice on this would be greatly appreciated, thanks!
Best

[teng-gao]

yes, the stack clone bar is meant to reflect uncertainty, and if it looks mixed then it suggests the level of uncertainty is high.

You can remake this plot using numbat_obj$plot_phylo_heatmap() while setting clone_stack = FALSE, and it will plot the maximum likelihood assignment for each cell. It might help with the visuals

https://kharchenkolab.github.io/numbat/reference/plot_phylo_heatmap.html