hpoPlot (version 1.0)

hpo.graph: Plot HPO Terms

Description

Function to display, or save to a PDF, a plot of sets of HPO terms.

Usage

hpo.graph(
	hpo.terms, 
	patients, 
	term.information.content = NULL, 
	term.population.frequency = NULL, 
	terms=NULL, 
	colouring.function = colouring.functions$get.frequency.based.colours, 
	labelling.function = labelling.functions$get.frequency.based.labels, 
	border.function = border.functions$get.no.borders, 
	size.function = size.functions$get.standard.sizes, 
	main.title = NULL, 
	draw.legend = FALSE, 
	filter.out.uninformative = FALSE, 
	filter.out.non.pa.terms = FALSE, 
	min.occs = 1, 
	nodeAttrs = NULL, 
	pdf.file.name = NULL, 
	pdf.height = 10, 
	pdf.width = NULL
)

Arguments

hpo.terms

An R-Object representing the HPO, as returned by get.hpo.terms.

patients

A list of character vectors of HPO terms, where typically each list item represents a patient. e.g. patients=list(A="HP:00000118")

term.information.content

The `Information-Content' (i.e. -log frequency) of the terms relevant to the plot as a named (by the HPO ID) vector in the context of a particular cohort of patients (as returned by get.cohort.informati

term.population.frequency

An alternative to the `term.information.content', the frequency of the terms relevant to the plot in the population, as opposed to in the sample to be plotted, as a named vector of values between 0 and 1. If both this and `term.information.content' are gi

terms

Character vector of HPO term codes for terms which are to appear in the plot. Defaults to NULL whereafter the terms in the plot are chosen automatically depending on the filtering options (for example `filter.out.uninformative').

colouring.function

A named vector of colours for the terms in the plot or a function which returns one (see colouring.functions).

labelling.function

A named vector of labels for the terms in the plot or a function which returns one (see labelling.functions).

border.function

A named vector of border colours for the terms in the plot or a function which returns one (see border.functions).

size.function

A named vector of node radii (in inches) for the terms in the plot or a function which returns one (see size.functions).

main.title

Title for the plot

draw.legend

Boolean to decide whether legend is drawn. NOTE: The legend drawn may intersect the plot.

filter.out.uninformative

Filter out uninformative nodes (i.e. nodes add no new information to the plot, given the presence of their children).

filter.out.non.pa.terms

Filter out nodes which are not descendants of the `Phenotypic abnormality' HPO-term.

min.occs

Filter out nodes which occur less than `min.occs' times in `patients'.

nodeAttrs

A custom Rgraphviz node attributes object which overrides any other graphical parameters passed to this function. Use this to set font size, font colour and more (for a full list see the Rgraphviz documentation).

pdf.file.name

File name. If null will plot to the current graphical device.

pdf.height

Height in inches of PDF created.

pdf.width

Width in inches of PDF created (if left NULL, the function will try to set this based on the pdf.height parameter and the number of leaves in the plot, so that the graph looks legible).

Examples

data(hpo)

	patients.character.vector <- 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" 
	)

	patients.of.interest <- term.set.list.from.character(hpo.terms, patients.character.vector)

	hpo.graph(
		hpo.terms=hpo.terms,
		patients=patients.of.interest,
		main.title="Test Plot",
		filter.out.uninformative=TRUE
	)