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--layout CLI param help confusing

See original GitHub issue

the help text for --layout is confusing - it should clearly state that not specifying a layout will make all embeddings in the dataset available, and that specifying layout names will restrict options to those specified.

Changes to be made:

CLI parameter --layout modified to accept N embedding names (rather than the current restriction of one). Any specified will present in the web UI. Default, if not specified, is to present all embeddings.
CLI parameter --layout changes to --embedding. Help and error text in the CLI change corresponding.
UI text changes from layout to embedding (eg, in the menu used to select an embedding)

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:17 (11 by maintainers)

Top GitHub Comments

1reaction

sidneymbellcommented, Aug 26, 2019

Is the difference in load time more than a few seconds? I think it’s worth a few seconds to have all the layouts available.

On Mon, Aug 26, 2019 at 2:34 PM Bruce Martin notifications@github.com wrote:

To clarify, --layout will reduce loading time, not rendering time. It just restricts the amount of data transferred from back-end to front-end at initialization time. For small or medium-sized datasets, the difference is probably immaterial…

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1reaction

sidneymbellcommented, Aug 22, 2019

I actually think this is outdated; now that we support any layout specified in adata.obsm['X_foo'], we could probably even just remove this argument. If we keep it, I’d be in favor of the changed functionality you propose where it specifies a default instead.

On Thu, Aug 22, 2019 at 10:38 AM Lia Prins notifications@github.com wrote:

@sidneymbell https://github.com/sidneymbell Do you have input or ideas for what would be better for the --layout option?

keep current functionality (specifying a layout via CLI means no other layouts are available in the UI) or

change functionality so that specifying a layout via CLI means that the specified layout is default when they open cellxgene, but they still have access to switching to any of the other available layouts through the UI’s “Layout choice” radio buttons

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