Add groupwise data to obs

[grst]

In GitLab by @szabogtamas on Feb 10, 2020, 13:00

When computing convergence, it seems plausible to add the convergence value (let us say log(1/singleton rate) for now) for a single cell given the grouping to obs and not only the singleton/duplicate/triplicate rates to uns.
The case would be similar with alpha diversity scores and maybe also clonal expansion.
If we add it, what rule should we follow for column names?

[grst]

In GitLab by @grst on Feb 11, 2020, 11:41

Sounds like a good idea to me. Then the data can easily be used to visualize it on a umap embedding also.

• I guess column names shouldn't be too long, but long enough that it's clear what they contain.
• Ideally, the column name can be customized using a function argument (I think it's called key_added in scanpy).
• Data should not be duplicated (if uns contains summaries and obs a per-cell value it's ok, but if it would contain exactly the same information, it should only be stored in one of obs and uns.)

[grst]

In GitLab by @grst on Mar 20, 2020, 18:12

For some of the computed metrics, this is definitely useful.
E.g. clonal expansion could also be nice to visualize on a umap plot.

[grst]

In GitLab by @grst on Mar 20, 2020, 18:13

changed title from Add {-any of groupwise data to both uns and obs as well?-} to Add {+ groupwise data to obs+}

[grst]

In GitLab by @grst on Mar 20, 2020, 18:13

assigned to @grst

[grst]

In GitLab by @grst on Mar 30, 2020, 11:07

mentioned in commit 8ce1265

[grst]

In GitLab by @grst on Mar 30, 2020, 11:20

closed via merge request !31

[grst]

In GitLab by @grst on Mar 30, 2020, 11:20

closed via merge request !29

[grst]

In GitLab by @grst on Mar 30, 2020, 11:20

mentioned in commit 28a1796

[grst]

In GitLab by @grst on Mar 30, 2020, 11:20

closed via commit 8ce1265