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Add examples for advanced data passing, e.g. how to pass x_attr/y_attr #643

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MUCDK opened this issue Jan 8, 2024 · 2 comments
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@MUCDK
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MUCDK commented Jan 8, 2024

          Can we create an issue for this?

Originally posted by @michalk8 in #633 (comment)

This was referenced Jun 11, 2024
@MUCDK
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MUCDK commented Jun 11, 2024

also mention that set_xy/x/y, and set_graph_xy exist, and point to the relevant examples.

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MUCDK commented Jun 11, 2024

main message: "show where we can fetch data from our anndata object"

  • fetch data from .X (e.g. if you wanna have raw counts)
  • fetch data from .layers (e.g. if you wanna have normalized counts)
  • fetch data from .obsm (e.g. if you wanna have PCA, but please do example with something else)

Use a FGW problem, and take different embeddings for all of them, e.g. with the MappingProblem:

  • x: normalized spatial (no callback here, but something pre-computed (but obv. link to callback))
  • y: PCA of all single-cel genes
  • xy: 50 most highly variables genes which are log1p normalized

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