hpoPlot (version 2.2)

get.hpo.graph: Get HPO graph object

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 = get.white.nodes,
  labels = get.simple.node.labels, borders = get.grey.borders,
  sizes = get.standard.sizes, font.sizes = rep(30, length(terms)),
  shapes = rep("circle", length(terms)), nodeAttrs = NULL)

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

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)
)