QC and filtering (icbi-lab#16)

* move position of QC notebook * Add function to filter outliers * WIP QC * update notebook * update qc notebook * fix sphinx warning * jupytext pre-commit * add pre-commit hook to detect merge conflicts * fix bib file * fix api page
vjmarteau · Apr 13, 2023 · e51b5f2 · e51b5f2
1 parent abdf4a1
commit e51b5f2
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Showing 14 changed files with 776 additions and 438 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -57,6 +57,7 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
+          - id: check-merge-conflict
     - repo: local
       hooks:
           - id: forbid-to-commit

diff --git a/docs/api.md b/docs/api.md
@@ -9,11 +9,11 @@
 .. autosummary::
     :toctree: generated
 
-    pl.plot_qc_metrics
-    pl.significance_heatmap
+    pp.is_outlier
 
     tl.fdr_correction
+    tl.scissor_wilcoxon_test
     tl.CpdbAnalysis
 
-    tl.scissor_wilcoxon_test
+    pl.significance_heatmap
 ```
diff --git a/docs/index.md b/docs/index.md
@@ -6,9 +6,9 @@
 :hidden: true
 :maxdepth: 1
 
-notebooks/01_qc.ipynb
 notebooks/02_seed_annotation.ipynb
 notebooks/03_merge.ipynb
+notebooks/03-2_qc.ipynb
 notebooks/04_integrate_scvi.ipynb
 notebooks/05_cell_type_annotation.ipynb
 

diff --git a/docs/notebooks/01_qc.ipynb b/docs/notebooks/01_qc.ipynb
diff --git a/docs/notebooks/01_qc.py b/docs/notebooks/01_qc.py