Open jwweii opened 1 month ago
Hi @jwweii thanks for reporting.
Regarding the empty prefix problem, this has been reported here: https://github.com/scverse/spatialdata-io/issues/212 and a solution has been developed from one of the user, and should be soon available in a PR.
Regarding the var_names_make_unique()
, we are aware of this and indeed calling the function is the way to go. But I understand that this could create confusion, so I will:
visium()
and visium_hd()
to fix the var names by default, but still letting the user disable the renaming.
I've encountered two issues when using the package:
To resolve this, I had to manually modify the file visium_hd.py, line 96, to include the sample prefix by changing the code to:
filename_prefix = f"{dataset_id}_" if dataset_id else ""
(I input dataset_id as "" in the argument)adata.var_names_make_unique()