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

Description Usage Arguments Value

Description

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

Usage

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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



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