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Fix heatmap passing of uns data to scanpy.pl.heatmap #110

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merged 4 commits into from
Sep 25, 2023
Merged

Fix heatmap passing of uns data to scanpy.pl.heatmap #110

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8c017cf
Update _chromosome_heatmap.py
jpintar Sep 25, 2023
19fe1d8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2023
bd407b4
Fix tmp_obs index type in chromosome_heatmap_summary
jpintar Sep 25, 2023
52ac04f
Merge branch 'main' into main
grst Sep 25, 2023
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12 changes: 2 additions & 10 deletions src/infercnvpy/pl/_chromosome_heatmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,6 @@ def chromosome_heatmap(
raise ValueError("'cnv_leiden' is not in `adata.obs`. Did you run `tl.leiden()`?")
tmp_adata = AnnData(X=adata.obsm[f"X_{use_rep}"], obs=adata.obs, uns=adata.uns)

# transfer colors from adata if present
if f"{groupby}_colors" in adata.uns:
tmp_adata.uns[f"{groupby}_colors"] = adata.uns[f"{groupby}_colors"]

# re-sort, as saving & loading anndata destroys the order
chr_pos_dict = dict(sorted(adata.uns[use_rep]["chr_pos"].items(), key=lambda x: x[1]))
chr_pos = list(chr_pos_dict.values())
Expand Down Expand Up @@ -145,6 +141,7 @@ def chromosome_heatmap_summary(
groups = adata.obs[groupby].unique()
tmp_obs = pd.DataFrame()
tmp_obs[groupby] = np.hstack([np.repeat(x, 10) for x in groups])
tmp_obs.index = tmp_obs.index.astype(str)

def _get_group_mean(group):
group_mean = np.mean(adata.obsm[f"X_{use_rep}"][adata.obs[groupby] == group, :], axis=0)
Expand All @@ -154,14 +151,9 @@ def _get_group_mean(group):
return group_mean

tmp_adata = sc.AnnData(
X=np.vstack([np.repeat(_get_group_mean(group), 10, axis=0) for group in groups]),
obs=tmp_obs,
X=np.vstack([np.repeat(_get_group_mean(group), 10, axis=0) for group in groups]), obs=tmp_obs, uns=adata.uns
)

# transfer colors from adata if present
if f"{groupby}_colors" in adata.uns:
tmp_adata.uns[f"{groupby}_colors"] = adata.uns[f"{groupby}_colors"]

chr_pos_dict = dict(sorted(adata.uns[use_rep]["chr_pos"].items(), key=lambda x: x[1]))
chr_pos = list(chr_pos_dict.values())

Expand Down