Atera WTA breast topology workflow#

pyXenium ships a fixed reproducibility workflow for the Atera WTA FFPE breast Xenium sample.

Core entrypoints:

  • pyXenium.cci.cci_topology_analysis

  • pyXenium.pathway.pathway_topology_analysis

  • pyXenium.pathway.compute_pathway_activity_matrix

  • pyXenium.validation.run_atera_wta_breast_topology

CLI usage#

pyxenium atera-wta-breast-topology \
  "Y:/long/10X_datasets/Xenium/Atera/WTA_Preview_FFPE_Breast_Cancer_outs" \
  --manuscript-mode

Python usage#

from pyXenium.validation import run_atera_wta_breast_topology

study = run_atera_wta_breast_topology(
    dataset_root=r"Y:\long\10X_datasets\Xenium\Atera\WTA_Preview_FFPE_Breast_Cancer_outs",
    manuscript_mode=True,
    manuscript_root="manuscript",
)

By default the workflow prefers precomputed topology anchors under:

<dataset_root>/sfplot_tbc_formal_wta/results

That directory should contain:

  • t_and_c_result*.csv

  • StructureMap_table*.csv

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