get_graph_matrix: Get all dependency matrices given a dependecy graph

In phenoscape/scate-shortcourse: Short Course on Phylogenetic Comparative Analysis of Integrated Anatomical Traits

Get all dependency matrices given a dependecy graph

Description

Construct dependency matrices and their correponding attributes

Usage

get_graph_matrix(graph)

Arguments

graph

igraph object of ontology terms

Details

$binary.matrices # intial binary matrices assigned to each node of graph $comb.matrices$matrix # combined matrix for each node $comb.matrices$state.string # vector of states [1] "00" "01" "10" "11" $comb.matrices$state.ident # specifies the order of ontology terms in each state [1] "UBERON:0007829" "UBERON:2000663" $comb.matrices$state.observable # ids and names of "observable" states. In red-blue tail notation refers to blue and red states $comb.matrices$state.hidden # ids and names of "hidden" states. In red-blue tail notation refers to "blue absent" and "red absent" $nodes.sorted # topologically sorted nodes $vertex.hier # hierrachy of the nodes

Value

List of matrices and their attributes

Examples

get_graph_matrix(g)

phenoscape/scate-shortcourse documentation built on Feb. 5, 2023, 12:59 a.m.