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support loading arbitrary layouts

See original GitHub issue

currently, 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)

Top GitHub Comments

1reaction

sidneymbellcommented, May 15, 2019

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

0reactions

bkmartinjrcommented, May 15, 2019

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.