get.hpo.graph: Get HPO graph object

In hpoPlot: Functions for Plotting HPO Terms

Description

Get HPO graph object

Usage

get.hpo.graph(hpo.terms, terms = apply.term.filters(hpo.terms = hpo.terms,
  plotting.context = plotting.context, term.filters = list()),
  plotting.context = NULL, colours = "white",
  labels = get.simple.node.labels, borders = "#FFFFFF00", sizes = 0.75,
  font.sizes = rep(30, length(terms)), shapes = rep("circle",
  length(terms)), nodeAttrs = NULL, arrowAttrs = list(color = "#000000"))

Arguments

hpo.terms	R-Object representation of HPO
terms	Character vector of HPO terms
plotting.context	List object with hpo.phenotypes slot for list of character vectors of terms
colours	Function to set the colours of the HPO nodes in the graph based on the plotting context, or a character vector of colours
labels	Function to set the labels of the HPO nodes in the graph based on the plotting context, or a character vector of node labels
borders	Function to set the borders of the HPO nodes in the graph based on the plotting context, or a character vector of border colours
sizes	Function to set the sizes of the HPO nodes in the graph based on the plotting context, or a numeric vector of node sizes
font.sizes	Function to set the font sizes of the text to be placed in the HPO nodes in the graph based on the plotting context, or an integer vector of font sizes
shapes	Function to set the shapes of the HPO nodes in the graph based on the plotting context, or a character vector of shape names (defaults to 'circle')
nodeAttrs	Pass nodeAttrs directly to rgraphviz plotting function
arrowAttrs	List of properties to set for arrows (note, these properties will be used for all arrow)

Value

graphAM S4 object

See Also

hpo.plot

Examples

data(hpo.terms)
phenotype.strings <- c(
	A="HP:0001382,HP:0004272,HP:0007917,HP:0004912,HP:0001596",
	B="HP:0001382,HP:0004272,HP:0002165,HP:0004800,HP:0004912",
	C="HP:0004800,HP:0001382,HP:0004912,HP:0007917,HP:0008743",
	D="HP:0001257,HP:0001382,HP:0007917,HP:0012623,HP:0002165",
	E="HP:0007917,HP:0004800,HP:0004272,HP:0001596,HP:0002165"
)

hpo.phenotypes <- term.set.list.from.character(phenotype.strings)

get.hpo.graph(
	hpo.terms=hpo.terms,
	plotting.context=list(hpo.phenotypes=hpo.phenotypes)
)

Example output

[1] "A graph with 73 nodes."

hpoPlot documentation built on May 2, 2019, 5:52 a.m.