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get_perturbation_paths

Finds and scores paths between the cell groups a perturbation gains (or loses with no lost parent) and the cell groups it loses, on a pathfinding graph.

get_perturbation_paths(
  perturbation_ccm,
  perturb_summary_tbl,
  pathfinding_graph,
  delta_log_abund_loss_thresh = 0
)

Arguments

  • perturbation_ccm
    A fitted genotype CCM (see fit_genotype_ccm()), passed through to the path-scoring step.

  • perturb_summary_tbl
    Per-cell-group loss/gain summary for this perturbation; must have cell_group, loss_when_present, and gain_when_present columns.

  • pathfinding_graph
    An igraph used for path search.

  • delta_log_abund_loss_thresh
    Minimum magnitude of loss_when_present/gain_when_present for a cell group to count as lost or gained (default 0).

Value

A tibble of scored paths between gained/parentless-lost cell groups and lost cell groups (one row per from/to pair with a path), or NA if no lost cell groups are present, no paths are found, or path search fails.

Details

get_perturbation_paths() finds shortest paths on pathfinding_graph from cell groups that are gained (or lost with no lost parent already in the loss set) to cell groups that are lost, then scores each path for how well it explains the perturbation's abundance changes — a way to trace a perturbation's lost cell states back to a plausible upstream origin along the lineage.