Open picciama opened 3 years ago
This has been worked on here: https://github.com/theislab/anndata/pull/342
The idea is to allow any vector from the anndata object to be used for coloring, but that PR seems a bit stalled at the moment. This would also be useful for providing parameters in other places, like regress_out
.
sc.tools
?sc.pl
?sc.external.*
?Quite often I need to color UMAPs based on features that are not part of
adata.X
butadata.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:
Clustering must not include these viral genes -> must be excluded from
X
. I don't want to store so many additional columns inobs
and I need to have these features separated in their own matrix for downstream analysis, which is why I want to useobsm
.Can we have sth. like this:
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
norvar.columns
, then check the keys inobsm
and use the entire dataframe behind this key.