sq.pp.filter_cells for SpatialData
#1011
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1011 +/- ##
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+ Coverage 66.63% 66.80% +0.16%
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Files 40 41 +1
Lines 6060 6160 +100
Branches 1015 1036 +21
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+ Hits 4038 4115 +77
- Misses 1662 1673 +11
- Partials 360 372 +12
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scverse#1045) * add numerical stability * simplify unnecessary parameters and arrays * Update src/squidpy/gr/_sepal.py Co-authored-by: Philipp A. <[email protected]> * add documentation --------- Co-authored-by: Philipp A. <[email protected]>
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…cverse#978) * Change niche flavor to cellcharter_simple and default distance = 3 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added warning message --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Tim Treis <[email protected]> Co-authored-by: Tim Treis <[email protected]>
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Fixes #1007.
Hi @timtreis ,
I changed some things compared to your PR: #967 . The things I changed:
min_counts, min_genes, max_counts, max_genessince all of them can be handled by the call ofsc.filter_cellsThe code from what I understand should be in the following logic.
sc.filter_cellsfilter the tables and update others based on that. If there is no actual filtering I think it would be best because we would assure same behavior withsc.filter_cellsWhat needs to be done:
Tests fails because scverse/spatialdata#946 needs to be merged first