plotOntologyFamily: Plot related ontologies in one hierarchical network plot

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Plot related ontologies in one hierarchical network plot

Description

Plot related ontologies in one hierarchical network plot

Usage

plotOntologyFamily(
  fam,
  data,
  plot.type = "complete",
  show.ids = FALSE,
  string.length = 18,
  legend.label.size = 1,
  legend.position = "topright",
  verbose = TRUE,
  n.cores = 1,
  reduce.edges = FALSE,
  font.size = 24
)

Arguments

fam	List of ontology IDs for the chosen family
data	Data frame if raw ontology data for the chosen cell type
plot.type	character (default="complete") How much of the family network should be plotted. Can be "complete" (entire network), "dense" (show 1 parent for each significant term), or "minimal" (only show significant terms)
show.ids	boolean (default=FALSE) Whether to show ontology IDs instead of names
string.length	integer (default=18) Length of strings for wrapping in order to fit text within boxes
legend.label.size	integer (default=1) Size of legend labels
legend.position	character vector (default="topright") Position of legend
verbose	boolean (default=TRUE) Print messages
n.cores	integer (default=1) Number of cores to use
reduce.edges	boolean (default=FALSE) Remove redundant edges in network
font.size	integer (default=24) Size of the font

Value

Rgraphviz object

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.