support loading arbitrary layouts
See original GitHub issuecurrently, cellxgene launch
allows the user to select from the standard layouts that scanpy uses, each of which is stored in .obsm
and prefaced with X_
.
If a user has another layout (e.g. spatial), they cannot load it into cellxgene.
suggested change: allow the user to use any layout stored in an .obsm
key with the syntax X_<layout>
preferred UX:
- let user pass layout to use into CLI
- if requested layout does not exist or no layout is passed in, inspect file and give user prompt with available layouts
Issue Analytics
- State:
- Created 4 years ago
- Comments:8 (8 by maintainers)
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Open to discussion (lots of reasonable interpretations here).
Unless specified by the user, I would try and default to (take the first one available):
X_umap
>X_tsne
>X_pca
Clarifying from discussion with @sidneymbell - the defaults above are for selecting a layout to display by default (ie, without any user input), not which layouts are available for user-selection.