Functions depending on igraph

Usage

make_igraph(population)

subtree(graph, nodes = integer(0L), trim = FALSE)

subgraph_upstream(graph, vids = integer(0L), trim = FALSE)

trim_root(graph)

internal_nodes(graph, nodes, sensitivity)

distances_from_origin(
  graph,
  nodes = sink_cells(graph),
  weights = numeric(0L),
  trim = FALSE
)

distances_upstream(
  graph,
  vids = integer(0),
  weights = numeric(0L),
  trim = FALSE
)

sink_cells(graph)

Arguments

population: tbl
graph: igraph
nodes: integer cell IDs
trim: whether to remove common ancestors older than MRCA.
vids: vertex IDs
sensitivity: minimum allele frequency
weights: A numeric or logical. Edge attribute "weight" is used if TRUE.

Details

make_igraph converts raw population tbl into graph.

subtree() and subgraph_upstream() extracts subgraph among terminal nodes.

trim_root() removes ancestral nodes older than MRCA.

internal_nodes selects major common ancestors above threshold.

distances_from_origin() and distances_upstream() are a shorthand of distances(..., mode = 2L).

sink_cells() returns the cell IDs of the sink nodes.