Bug in diffusion map plotting in 1.9.1?

[cbravo93]

• [ x] I have checked that this issue has not already been reported.
• [ x] I have confirmed this bug exists on the latest version of scanpy.
• [ ] (optional) I have confirmed this bug exists on the master branch of scanpy.

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Hi!

When running sc.pl.diffmap with 1.8.2 in my object I get a nice diffusion map plot: However, when using the same function with 1.9.1 in exactly the same object (with exactly the same 'X_diffmap') I get an awful plot:

Any idea what is going on? This only affects plotting (also tried using sc.pl.embedding), the dpt function gives the same results for example.

Thanks!

C

[mmyoung]

I am also facing the same issue here, have you got any solutions yet? Thanks.

[cbravo93]

I just reverted to scanpy 1.8.2 for now . C

[Koncopd]

@cbravo93 @mmyoung a quick fix is to do adata.obsm["X_diffmap_"] = adata.obsm["X_diffmap"][:, 1:] sc.pl.embedding(adata, "diffmap_")

[RainboWu]

Thanks for @Koncopd 's advice