Fix using custom layer with highly_variable_genes #2302
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Codecov Report
@@ Coverage Diff @@
## master #2302 +/- ##
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Coverage 71.82% 71.82%
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Files 98 98
Lines 11539 11539
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Hits 8288 8288
Misses 3251 3251
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lazappi
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Aug 12, 2022
* origin/fix-2230: Fix using custom layer with highly_variable_genes (scverse#2302) [pre-commit.ci] pre-commit autoupdate (scverse#2303) [pre-commit.ci] pre-commit autoupdate (scverse#2289)
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ivirshup
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Feb 16, 2023
* Fix using custom layer with highly_variable_genes * Add tests * Add release note * Move release note to correct section
ivirshup
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* Backport PR #2414: matplotlib 3.7 compat * fix scrublet * Update visium default plot for matplotlib 3.7 * Update hashsolo docstrings * skip plotting test that changed on mpl 3.7 if mpl < 3.7 is installed * Fix hashsolo docs (again) * update anndata-dev tests to install anndata test deps * Temporarily set warnings as errors to False for doc builds * Release notes * Fix using custom layer with highly_variable_genes (#2302) * Fix using custom layer with highly_variable_genes * Add tests * Add release note * Move release note to correct section * Format release notes * Add check for number of normalized dispersions (#2231) * Add check for number of normalized dispersions In sc.pp.highly_variable_genes() when flavor='cell_ranger' and n_top_genes is set check that enough normalized dispersions have been calculated and if not raise a warning and set n_top_genes to the number of calculated dispersions. Fixes #2230 * Use .size instead of len() * Add test for n_top_genes warning * Add release note * Remove blank line Co-authored-by: Isaac Virshup <ivirshup@gmail.com> --------- Co-authored-by: Isaac Virshup <ivirshup@gmail.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
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This PR takes off where #2183 went stale.