Add option to change plotting basis

[cenk-celik]

Thank you for developing cell2fate—it's been incredibly useful for my research!

I was wondering if it would be possible to add an option to change the embedding basis for plotting functions like compute_and_plot_total_velocity() and plot_module_summary_statistics(). While umap is a great default, my data works better with phate embeddings, and having this flexibility would improve the interpretation of results.

Thanks in advance for considering this feature request!

[AlexanderAivazidis]

Thanks for your suggestion! It makes sense, I will have a look today if this can be done in a relatively straightforward manner.

[cenk-celik]

Thanks! Appreciate your efforts in advance. For now, I just do the following trick without having to set a basis in the functions:

adata.obsm["X_umap"] = adata.obsm["X_phate"]

However, I'd like to keep X_umap as well.

[AlexanderAivazidis]

Oh I see! Then you could also just do this:

adata.obsm["X_umap_old"] = adata.obsm["X_umap"].copy()
adata.obsm["X_umap"] = adata.obsm["X_phate"]

And when you want to plot with the original UMAP basis again you substitute it back in:

adata.obsm["X_umap"] = adata.obsm["X_umap_old"].copy()