plotOntoNetwork: Plot Network of Ontology Clusters

In altintasali/ontoClust: Cluster Gene Ontology Terms

Description

Plot Network of Ontology Clusters

Usage

plotOntoNetwork(
  oc,
  layout = "kk",
  size_ontology = 3,
  size_label_ontology = 2,
  alpha_edge = 0.2,
  alpha_node = 1,
  facet_by = NULL,
  background = TRUE,
  label_n = 4
)

Arguments

oc	ontoClust object. The output of getOntoClust
layout	Network layout. See ggraph for details. Default is "kk". Some options are 'kk', 'dh', 'circle', 'gem', 'graphopt', 'grid', 'mds', 'randomly', 'fr', 'drl', 'lgl', 'nicely'
size_ontology	Size of ontology (node) terms. Default is 3.
size_label_ontology	Size of ontology (node) term labels. Default is 2.
alpha_edge	Transparency parameter for edges (link communities). Default is 0.2.
alpha_node	Transparency parameter for nodes (ontology clusters). Default is 1 (fully opaque).
facet_by	Facets to draw. Default is NULL, thus no facets are drawn. It can be 'ontology_cluster' or 'link_community'
background	Keep the nodes/edges in the background when facetted. Default is TRUE. If FALSE, only edges/nodes that connects each ontology-cluster/link-community will be drawn.
label_n	Print top words to the facet labels. Default is 4. If NULL, NA or <=0, no words will be labelled.

Value

ggraph plot

Examples

## Not run: 
ontology.id <- sample_data$GOBP$ID[1:50]
network <- createOntologyNetwork(ontology.id, method = "jaccard", weighted = FALSE)
lc <- getLC(network)
oc <- getOntoClust(lc)
plotOntoNetwork(oc)
plotOntoNetwork(oc, facet_by = c("ontology_cluster", "link_community")[1])
plotOntoNetwork(oc, facet_by = c("ontology_cluster", "link_community")[1], background = TRUE)

## End(Not run)

altintasali/ontoClust documentation built on Dec. 19, 2021, 1:36 a.m.