summary bug
abyssum opened this issue · comments
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ValueError Traceback (most recent call last)
<ipython-input-194-09942ce7d463> in <module>
----> 1 cnv.pl.chromosome_heatmap_summary(adata_copykat[adata_copykat.obs["cnv_leiden"].isin(["10", "8", "6"]), :], groupby = "cnv_leiden")
~/.local/lib/python3.8/site-packages/infercnvpy/pl/_chromosome_heatmap.py in chromosome_heatmap_summary(adata, groupby, use_rep, cmap, figsize, show, save, **kwargs)
145 tmp_obs = pd.DataFrame()
146 tmp_obs[groupby] = np.hstack([np.repeat(x, 10) for x in groups])
--> 147 tmp_adata = sc.AnnData(
148 X=np.vstack(
149 [
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
305 self._init_as_view(X, oidx, vidx)
306 else:
--> 307 self._init_as_actual(
308 X=X,
309 obs=obs,
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
516 _move_adj_mtx({"uns": self._uns, "obsp": self._obsp})
517
--> 518 self._check_dimensions()
519 self._check_uniqueness()
520
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _check_dimensions(self, key)
1767 key = {key}
1768 if "obs" in key and len(self._obs) != self._n_obs:
-> 1769 raise ValueError(
1770 "Observations annot. `obs` must have number of rows of `X`"
1771 f" ({self._n_obs}), but has {self._obs.shape[0]} rows."
ValueError: Observations annot. `obs` must have number of rows of `X` (3), but has 30 rows.
I suspect it's due to the matrix being dense.
This should totally be supported, I'll create a fix after the holiday
@abyssum, this should now work in infercnvpy==0.1.2