graph: Functions depending on igraph

make_igraphR Documentation

Functions depending on igraph

Description

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.


heavywatal/tumorr documentation built on Aug. 25, 2024, 5:37 p.m.