hpoPlot (version 2.2)

hpo.plot: Plot HPO graph object

Description

Plot HPO graph object

Usage

hpo.plot(hpo.terms, terms = apply.term.filters(hpo.terms = hpo.terms,
  plotting.context = plotting.context, term.filters = list()),
  plotting.context = NULL, hpo.phenotypes = NULL, term.frequencies = NULL,
  colours = rep("cyan", length(terms)), labels = get.simple.node.labels,
  borders = get.no.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

hpo.phenotypes

List of HPO term character vectors

term.frequencies

Numeric vector of population frequencies of terms (named by term codes)

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

...

Extra arguments to pass to plot

Value

• Plots graph

See Also

get.hpo.graph

Examples

data(hpo.terms)
hpo.plot(
	hpo.terms=hpo.terms,
	terms=get.ancestors(hpo.terms,
		c("HP:0001382","HP:0004272","HP:0007917","HP:0004912","HP:0001596"))
)