Comments (9)
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 andobs
a per-cell value it's ok, but if it would contain exactly the same information, it should only be stored in one ofobs
anduns
.)
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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.
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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+}
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In GitLab by @grst on Mar 20, 2020, 18:13
assigned to @grst
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In GitLab by @grst on Mar 30, 2020, 11:07
mentioned in commit 8ce1265
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In GitLab by @grst on Mar 30, 2020, 11:20
closed via merge request !31
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In GitLab by @grst on Mar 30, 2020, 11:20
closed via merge request !29
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In GitLab by @grst on Mar 30, 2020, 11:20
mentioned in commit 28a1796
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In GitLab by @grst on Mar 30, 2020, 11:20
closed via commit 8ce1265
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Related Issues (20)
- tl.define_clonotypes within_group parameter returns ValueError HOT 1
- Integrate TCRdist3 HOT 5
- Retrieving specific portions of the Immune Receptor beyond the junction (or CDR3). HOT 2
- ir_dist alignment stuck HOT 4
- IEDB database cdr3_aa stored as junction_aa HOT 10
- Unclear default value for the Hamming Distance cut-off HOT 1
- Dandelion interoperability
- Where has UMI count for AIR chains gone? HOT 1
- Large dataset tutorial
- Make sure axes of nextwork plots don't have any ticks
- Add the Morisita-Horn index for repertoire overlap similarity scores HOT 1
- Sorting logic in `index_chains()` HOT 3
- Community tutorial page
- ir.tl.ir_query fails with error 'ValueError: max_workers must be greater than 0' HOT 1
- ir.tl.clonotype_modularity - ValueError: Length of values does not match length of index HOT 2
- "read_10x_vdj" not loading data properly HOT 2
- clone definition purely using CDR3 sequence HOT 1
- Optimize TCRdist metric HOT 1
- When running 'ir.tl.define_clonotypes' on MacOS14.4.1, I've got an Error:module 'os' has no attribute 'sched_getaffinity' HOT 2
- TypeError: join() got an unexpected keyword argument 'validate' HOT 9
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