Decompose a Wedge's two hub paths into per-edge ligand-receptor contributions

A Wedge (see calculateWedges()) sums two directed 2-hop paths through hub j: i -> j -> k and k -> j -> i. Since Wedges multiply their two edges together rather than sum them, there is no single well-defined "share of the Wedge score" attributable to one edge's ligand-receptor pair alone – instead, this decomposes each of the 4 edges across both paths separately via computeLRContributions() (bundle = FALSE, one direction per edge), so PctOfTotal in the result is relative to each edge's own kernel value.

Usage

computeWedgeLRContributions(
  Lmatrix,
  Rmatrix,
  Cmatrix,
  LRmatrix,
  celltypes,
  i,
  j,
  k,
  Dcell = Cmatrix,
  patient_names = NULL,
  top_n = NULL
)

Arguments

Lmatrix, Rmatrix, Cmatrix, LRmatrix

Same inputs as compute_kernel().

celltypes

Character vector of cell-type names, in the row order of Lmatrix/Rmatrix/columns of Cmatrix.

i, k

Cell-type names for the wedge's two leaves.

j

Cell-type name for the wedge's hub.

Dcell

Patient-by-cell-type abundance matrix used to scale raw contributions to the same units as calculateDirect()'s raw score. Defaults to Cmatrix.

patient_names

Optional character vector of patient labels, matching the patient order in LRmatrix. Defaults to Patient_1, Patient_2, ...

top_n

Optional; if given, keep only the top top_n ligand-receptor pairs per patient (by Contribution).

Value

A data frame like computeLRContributions()'s (pooled across the 4 edges), with an added Path column ("i -> j -> k" or "k -> j -> i", using the actual cell-type names).