get.pop.frequency.based.colours: Function to colour HPO nodes in plot with colours based on...

In hpoPlot: Functions for Plotting HPO Terms

Description

Function to colour HPO nodes in plot with colours based on information content/frequency of terms with respect to population

Usage

get.pop.frequency.based.colours(hpo.terms, terms, plotting.context,
  colourPalette = colorRampPalette(c("Yellow", "Green", "#0099FF"))(10),
  terms.freq = if (is.null(plotting.context$frequency))
  exp(-plotting.context$information[terms]) else plotting.context$frequency,
  max.colour.freq = max(terms.freq), min.colour.freq = min(terms.freq))

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
colourPalette	Character vector of colours for the different information contents of the terms to be plotted, going from rare to common
terms.freq	Numeric vector of frequencies of terms in plot, named by term
max.colour.freq	Numeric value in [0, 1] giving the maximum frequency (to which the dullest color will be assigned)
min.colour.freq	Numeric value in [0, 1] giving the minimum frequency (to which the brightest color will be assigned)

Value

Character vector of colours, named by term

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