Closed scottgigante-immunai closed 1 year ago
The only isolated label is t_cell which only has seven cells. This doesn't seem like a good metric.
t_cell
>>> import openproblems >>> adata = openproblems.tasks.batch_integration_embed.datasets.pancreas_batch() >>> from scib.metrics.isolated_labels import * >>> isolated_labels = get_isolated_labels( ... adata, label_key="labels", batch_key="batch", iso_threshold=None, verbose=True ... ) isolated labels: no more than 4 batches per label >>> isolated_labels ['t_cell'] >>> adata.obs['labels'].value_counts() alpha 5493 beta 4169 ductal 2142 acinar 1669 delta 1055 gamma 699 activated_stellate 464 endothelial 313 quiescent_stellate 193 macrophage 79 mast 42 epsilon 32 schwann 25 t_cell 7 Name: labels, dtype: int64
The only isolated label is
t_cell
which only has seven cells. This doesn't seem like a good metric.