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static plotting for spatial data #437

Merged
merged 253 commits into from
Apr 14, 2022
Merged

static plotting for spatial data #437

merged 253 commits into from
Apr 14, 2022

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giovp
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@giovp giovp commented Dec 5, 2021 •
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Description

Add :func:squidpy.pl.spatial_scatter and :func:squidpy.pl.spatial_segment to statically plot spatial omics data.

TODO

  • add segmentation plotting capabilities Plotting values on top of segmentation mask #427
  • add some type of behaviour for alpha in continuous values. The reason for this is that if with umap you don't care to see points where the value is e.g. 0 (and you can just subset adata), in spatial you do cause you still want to see the full tissue (and this doesn't happen by proxy if you subset adata, cause it also crop the tissue). Not super sure how to handle it yet.
  • saving
  • docs
  • tests

closes #242 #247 #444

michalk8 and others added 13 commits September 16, 2021 22:21
@michalk8
Merge pull request #418 from theislab/fix/update-contributing
9845461 
Fix/update contributing
@michalk8
Fix patching ForwardRef when generating docs
9cca775
@michalk8
Require numba>=0.52.0 (#420)
019a1e1
@michalk8 @actions-user
[auto][ci skip] Generate news fragment (#420)
b30c3c2
@michalk8
Fix CI cron job, remove cond in newsgen (#424)
f5ee6dd 
* Fix CI cron job, remove cond in newsgen

* Less flaky dataset download test, fix linting
@michalk8 @actions-user
[auto][ci skip] Update dev release notes (#424)
2cae246
@michalk8
Fix None in ligrec source/target (#434)
21b59d7 
* Drop NAs in interactions

* Regenerate failing figures
@michalk8 @actions-user
[auto][ci skip] Generate news fragment (#434)
a7419bc
@michalk8 @actions-user
[auto][ci skip] Update dev release notes (#434)
be45fab
@giovp
allow Key.uns.library_id to return list
f825d62
@giovp
fix logic for Kye.uns.library_id
172f905
@giovp
add Key.uns.image_id
0d5fbaa
@giovp
fix logic Key.uns.image_id
e864116
@giovp giovp changed the base branch from master to dev December 5, 2021 19:52
@giovp giovp mentioned this pull request Dec 16, 2021
Closed
giovp and others added 21 commits April 14, 2022 12:10
@michalk8 michalk8 merged commit e83d072 into master Apr 14, 2022
michalk8 added a commit that referenced this pull request Apr 14, 2022
@michalk8 @github-actions
[auto][ci skip] Generate news fragment (#437)
cc9a899
michalk8 added a commit that referenced this pull request Apr 14, 2022
@michalk8 @github-actions
[auto][ci skip] Update release notes (#437)
de9a1c4
This was referenced Apr 19, 2022
Closed
Closed
@giovp giovp deleted the plspatial branch April 20, 2022 12:56
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Reviewers

@ivirshup ivirshup ivirshup left review comments

@michalk8 michalk8 michalk8 requested changes

@hspitzer hspitzer Awaiting requested review from hspitzer

@AnnaChristina AnnaChristina Awaiting requested review from AnnaChristina

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Successfully merging this pull request may close these issues.

Plotting values on top of segmentation mask Add scale information to plots
7 participants
@giovp @hspitzer @AnnaChristina @ivirshup @michalk8 @dcjones @dnjst