Closed adamgayoso closed 5 years ago
We could add back phonograph support as follows
import scanpy.external as sce
result = sce.tl.phenograph(adata.obsm['X_pca'], k = 30)
In fact we should make it an option so that we can always use the original method. This would also involve making the standard scaling an option.
We could add back phonograph support as follows
import scanpy.external as sce result = sce.tl.phenograph(adata.obsm['X_pca'], k = 30)
In fact we should make it an option so that we can always use the original method. This would also involve making the standard scaling an option.
I added this, but not through the external scanpy module. I added back what we had before.
@JonathanShor This is good to squash into dev. The only thing that is missing is that your PhenoGraph actually doesn't have a verbose or verbosity argument. So, if you choose to use_phenograph
and verbose is False
then Pheno will still print stuff out.
Scanpy backend implemented
tqdm
for progress bar