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Is your feature request related to a problem? Please describe.
In scirpy, I have a custom extension of "pl.embedding" that plots clonotype networks. Similar to the pl.embedding functions in muon and scanpy, nodes can be colored by either variables from obs, or by genes stored in X/raw/layers.
Muon provides a mechanism (which is currently somewhat broken, see #96) to retrieve values from either of the slots by specifying keys such as "gex:CD8A", "gex:sample", "patient" together with the parameters use_raw, and layer.
Alternatives
Maybe this should even be a method in MuData?
MuData.get("gex:CD8A")
Additional context
With scirpy v0.13, scirpy introduces support for MuData. Previously everything was in a single AnnData object, therefore this wasn't a problem before.
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
In scirpy, I have a custom extension of "pl.embedding" that plots clonotype networks. Similar to the
pl.embedding
functions in muon and scanpy, nodes can be colored by either variables fromobs
, or by genes stored inX
/raw
/layers
.Muon provides a mechanism (which is currently somewhat broken, see #96) to retrieve values from either of the slots by specifying keys such as
"gex:CD8A"
,"gex:sample"
,"patient"
together with the parametersuse_raw
, andlayer
.To achieve the same, I duplicated a lot of code from
mu.pl.embedding
into scirpy.To avoid this, it would be helpful to have this as a public function in muon, e.g.
Alternatives
Maybe this should even be a method in MuData?
Additional context
With scirpy v0.13, scirpy introduces support for MuData. Previously everything was in a single AnnData object, therefore this wasn't a problem before.
The text was updated successfully, but these errors were encountered: