I am trying to load some Visium data following the tutorial. In there, I see that the data is loaded as adata1 = sdm.datasets.dataset.melanoma(), I thought that I could just do adata = sc.read_visium("visium_ov_orig") to load my own files(using a Visium h5 file, this can be replicated with this file ), but then, I am getting errors in other parts of the tutorial, it starts failing when I call:
sdm.extract_lr(adata, 'human', min_cell=3)
with the error:
pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects
Is there a different way to load this data? I tried checking the codebase and couldn't find a method that seemed more suitable.
Hello,
Thank you for sharing the package.
I am trying to load some Visium data following the tutorial. In there, I see that the data is loaded as
adata1 = sdm.datasets.dataset.melanoma(), I thought that I could just doadata = sc.read_visium("visium_ov_orig")to load my own files(using a Visium h5 file, this can be replicated with this file ), but then, I am getting errors in other parts of the tutorial, it starts failing when I call:sdm.extract_lr(adata, 'human', min_cell=3)with the error:pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objectsIs there a different way to load this data? I tried checking the codebase and couldn't find a method that seemed more suitable.
Thank you