onto_plot: Get 'ontology_plot' object

In ontologyPlot: Visualising Sets of Ontological Terms

Description

A convenience wrapper for the get_ontology_plot function, enabling functions to be passed to generate graphical parameters for terms automatically.

Usage

onto_plot(ontology, term_sets = NULL, frequencies = NULL,
  terms = remove_uninformative_terms(ontology, term_sets),
  edge_attributes = list(color = "#000000", lty = "solid"),
  fillcolor = "powderblue", label = simple_labels, color = "transparent",
  width = 0.75, fontsize = 30, style = "filled", fixedsize = "true",
  shape = "circle", ...)

Arguments

ontology	ontology_index object
term_sets	List of character vectors of ontological term IDs
frequencies	Numeric vector of term frequencies named by term IDs
terms	Character vector of ontological terms
edge_attributes	List of properties to set for arrows (note, these properties will be used for all arrow).
fillcolor	Character vector of colours to fill nodes corresponding to terms with. Alternatively a function to set the colours of the nodes in the graph based on term_sets.
label	Character vector of labels (or function to set them).
color	Character vector of colours for borders of nodes representing terms (or function to set them).
width	Numeric vector of widths for nodes (of function to set them).
fontsize	Numeric vector of font sizes for the text to be placed in the nodes (or function to set them).
style	Display style for nodes, defaults to "filled".
fixedsize	Character indicating whether nodes should be fixed size, "true", or adjusted to fit around the contained text, "false".
shape	Character vector of shape names for nodes (or function to set them). Defaults to "circle".
...	Other node attributes for dot format.

Value

ontology_plot object.

See Also

get_ontology_plot, write_dot

Examples

library(ontologyIndex)
data(hpo)
hpo_phenotypes <- c(
	A=c("HP:0001382","HP:0004272","HP:0007917","HP:0004912","HP:0001596"),
	B=c("HP:0001382","HP:0004272","HP:0002165","HP:0004800","HP:0004912"),
	C=c("HP:0004800","HP:0001382","HP:0004912","HP:0007917","HP:0008743"),
	D=c("HP:0001257","HP:0001382","HP:0007917","HP:0012623","HP:0002165"),
	E=c("HP:0007917","HP:0004800","HP:0004272","HP:0001596","HP:0002165")
)

onto_plot(
	ontology=hpo,
	term_sets=hpo_phenotypes
)

Example output

ontologyPlot documentation built on Feb. 10, 2021, 5:06 p.m.