scverse/pertpy-tutorials

Bugs in Distance metrics tutorial

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In it's current version, the Distance metrics tutorial throws several errors. Most of them can be easily fixed by implementing the following things:

  • Remove verbose as a parameter from pairwise method whenever it's used in the tutorial
  • Specify that 'X_pca' is the obsm_key parameter when initializing a Distance object (obsm_key='X_pca')
  • Use correct distance name: There is one section titled PseudobulkDistance and a Distance object is initialized with the distance 'pseudobulk'. This distance, however, doesn't exist, hence an error is thrown. Is it possible that pseudobulk was renamed and is now called euclidean?

All those things are easily fixed, I just need conformation on the distance that is supposed to be used in the Pseudobulk section.

@Lilly-May yes, it was indeed renamed to what you said