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Merged
LuLeom merged 4 commits into from
Jul 30, 2026
Merged

Compute average_batch_r2 per cell type #127

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77ae355
compute average_batch_r2 per cell type
rcannood Jul 28, 2026
9cdefb0
update changelog
rcannood Jul 28, 2026
f119b33
fix changelog spacing
rcannood Jul 28, 2026
fc5efe3
Merge branch 'main' into fix-average-batch-r2-celltype
ghar1821 Jul 30, 2026
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -248,3 +248,7 @@
as scalars instead of lists, as required by `file_score.yaml` (PR #130).

* Clean up stale mock parameters and dead code (PR #133).


* Fix bug in `average_batch_r2` where the R2 was computed on all cell types of a donor at once
instead of on each cell type separately (PR #127).
4 changes: 2 additions & 2 deletions src/metrics/average_batch_r2/script.py
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Expand Up @@ -60,13 +60,13 @@
s2_view_ct = s2_view[s2_view.obs["cell_type"] == ct]
if (
s1_view_ct.shape[0] < 20 or s2_view_ct.shape[0] < 20
): # Skip Rˆ2 calculation if there are less than 10 cells
): # Skip Rˆ2 calculation if there are less than 20 cells
print(
f"Warning: Rˆ2 not computed for donor {donor} cell type {ct}. Too few cells were present: {s1_view_ct.shape[0]} for split 1 and {s2_view_ct.shape[0]} for split 2"
)
continue

r2_list, marker_list = batch_r2(s1_view, s2_view)
r2_list, marker_list = batch_r2(s1_view_ct, s2_view_ct)

marker_list = [ct + "_" + donor + "_" + x for x in marker_list]
r2_info = [*r2_info, *marker_list]
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