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hpoPlot (version 2.2)

Functions for Plotting HPO Terms

Description

Collection of functions for manipulating sets of HPO terms and plotting them with a various options.

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Version

Install

install.packages('hpoPlot')

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Version

2.2

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

August 26th, 2015

Functions in hpoPlot (2.2)

get.node.friendly.long.names

Split up the HPO term descriptions so they fit in nodes for plot

mpo.terms

MPO Terms object

get.white.nodes

Function to colour HPO nodes in plot white

term.set.list.from.character

Get list of character vector of HPO terms, given character vector of comma separated terms

remove.terms.with.less.than.n.occurrences

Remove terms with less than certain number of occurrences

get.term.descendancy.matrix

Get logical descendancy matrix for set of terms

hpoPlot

Functions for Plotting HPO Terms

get.term.adjacency.matrix

Get an adjacency for set of HPO terms

remove.non.pa.terms

Remove terms not descending from phenotypic abnormality

get.frequency.based.sizes

Function to size HPO nodes in plot based on frequency of occurrence in phenotypes

get.hpo.graph

Get HPO graph object

exclude.branch

Exclude terms descending from particular term from a character vector of terms

get.case.based.labels

Function to label HPO nodes in plot to indicate to which phenotypes each of the terms belong

get.ancestors

Get set of all ancestors of set of terms

get.shortened.names

Get human readable, shortened (where possible) HPO term names

get.mpo.to.hpo

Get MPO to HPO R-Object

hpo.terms

HPO Terms object (based on version 887 of the HPO)

get.significance.based.sizes

Function to size HPO nodes in plot with colours based on significance of seeing this many of each term in phenotypes

get.code.node.labels

Function to label HPO nodes in plot with just HPO code

get.no.borders

Function to border HPO nodes in plot with transparent borders

get.term.info.content

Get information content of each term in a set of phenotypes

setDimNames

setNames for arrays...

apply.term.filters

Apply a list of term filters to a given plotting context

get.simple.node.labels

Function to label HPO nodes in plot with just node description

get.pop.frequency.based.colours

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

prune.branch

Prune all terms descending from given term down to that term and ensure no degeneracy

get.frequency.based.labels

Function to label HPO nodes in plot based on frequency of occurrence in phenotypes

simpleCap

Capitalise words in character vector

get.term.pseudo.adjacency.matrix

Get an adjacency to MRCA matrix for set of HPO terms

get.case.based.colours

Function to set colours of HPO nodes in plot to distinguish terms belonging to different sets of phenotypes

get.informative.node.labels

Function to label HPO nodes in plot with node description and information content

n.most.frequent.terms

Select most frequently annotated terms from a set of phenotypes

get.frequency.based.colours

Function to colour HPO nodes in plot with colours based on frequency with which terms appear in phenotypes

get.term.frequencies

Get frequency of each term in a set of phenotypes

get.hpo.terms

Gets HPO R-Object

p.values.for.occurrence.of.term.in.group

Get p-values for observing at least as many of each term as have been in phenotypes given information content

get.case.term.matrix

Get a matrix with columns of hpo terms and rows of patients,

remove.uninformative.terms

Get a minimal set of terms which can be used to partition a set of phenotypes

calibrate.sizes

Function to scale sizes of terms between two given limits

get.grey.borders

Function to border HPO nodes in plot with grey borders

get.full.labels

Function to label HPO nodes in plot with full labels

get.ontology

Get R-Object representation of ontology from obo file

get.standard.sizes

Function to size HPO nodes in plot 0.75 inches across

clean.terms

Remove redundant/implied terms

mpo.to.hpo

Object containing data for mapping between MPO and HPO

swap.out.alt.ids

Remove alternate/deprecated HPO term IDs and swap for new ones

hpo.plot

Plot HPO graph object

intersection.with.branches

Intersect set of terms with branches of HPO

get.descendants

Get set of all descendants of single term

remove.links

Remove terms with exactly one parent and child from plot

remove.uninformative.for.plot

Remove uninformative terms (fitting plotting filter format)