get_relative_ont_level: Get relative ont level (for terms in a connected component of...

In ovrhuman/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Description

When plotting subsets of the HPO data as a network plot, there is often more than one connected component to be plotted (i.e. sections of the graph are not connected by any edges). To map the ontology level to the size of nodes (such that high up terms are bigger than low level terms). This was made to find the relative ontology level with respect to other terms in its connected component so that each connected section of the plot would have the same size for its root node. It would also be possible to just use absolute ontology level, so that "Phenotypic abnormality" would always be the largest datapoint etc.

Usage

get_relative_ont_level(phenotype, phenoAdj, hpo)

Arguments

phenotype	HPO term Id <string>
phenoAdj	A adjacency matrix (produced by the adjacency_matrix function)
hpo	The HPO ontology data object

Value

A integer representing the relative ontology level of a term within a connected component of a subset of the HPO.

ovrhuman/HPOExplorer documentation built on Dec. 22, 2021, 5:21 a.m.