Did not find X_scvi in .obsm.keys().

[dxl3742]

Hi Kelvin,
Great work on the package!
I want to run the trajectory analysis on my seurat object, which I have converted and preprocessed according to your instructions.
however I have run into this bug:

sc.pp.neighbors(adata, use_rep="X_scvi", n_neighbors=50)
ValueError: Did not find X_scvi in .obsm.keys(). You need to compute it first.
print(adata.obsm.keys())
KeysView(AxisArrays with keys: X_harmony, X_pca, X_umap)

How do I fix this? Any help would be appreciated, thanks in advance!

[zktuong]

Hi @dxl3742,

Thanks for the interest! Yea should swap that out with the keys you have, which should be either X_harmony or X_pca.

For example:

sc.pp.neighbors(adata, use_rep="X_harmony", n_neighbors=50)

Having said, that, if you already have a neighborhood graph in your .obsm (that you used for your normal analysis), you can skip this step and continue with the remaining steps.