Allow using arbitrary vectors in plotting (not only `obs` columns)
@flying-sheep is already working on this.
Since Oct 30, 2025.
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
Quite often I need to color UMAPs based on features that are not part of adata.X but adata.obsm for the reason that they are special. E.g. KO data with gRNAs versus endogenes/ target genes, or viral genes versus edogenes.
Example use case:
- Cluster cells based on endogenes
- UMAP and color by a bunch of viral genes
Clustering must not include these viral genes -> must be excluded from X.
I don't want to store so many additional columns in obs and I need to have these features separated in their own matrix for downstream analysis, which is why I want to use obsm.
Can we have sth. like this:
sc.pl.umap(adata, color='viral_genes') # adata.obsm['viral_genes'] is a pandas.DataFrame ?
It shouldn't be overcomplicated I think, since this only involves an additional check: if the elements in the color arg list are not found in obs.columns nor var.columns, then check the keys in obsm and use the entire dataframe behind this key.
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