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Add a gene_symbols parameter to `render_shapes` and `render_points`

Open grst opened this issue 1 year ago • 2 comments

It would be great to have a gene_symbols argument to render_shapes and render_points, similar to what scanpy has in all (most?) plotting functions.

The goal is being able to use ensembl identifiers are var_names, while retaining the possibility to conveniently make plots by gene symbols, which are stored in another column in adata.var.

Possible alternatives: Instead of passing this to the function call, there could be a per-spatialdata configuration option which columns in .var to lookup when a color is specified.

grst avatar Apr 08 '24 12:04 grst

Hey Gregor, sorry, don't fully get it yet. So you essentially want to store your data using ENSEMBL IDs for precision, but then use aliases for them downstream for convenience?

timtreis avatar Apr 16 '24 15:04 timtreis

exactly. This is already supported in by most scanpy functions.

grst avatar Apr 16 '24 16:04 grst