# Functions for Plotting HPO Terms

## Documentation for package ‘hpoPlot’ version 2.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

apply.term.filters | Apply a list of term filters to a given plotting context
calibrate.sizes | Function to scale sizes of terms between two given limits
clean.terms | Remove redundant/implied terms
exclude.branch | Exclude terms descending from particular term from a character vector of terms
get.ancestors | Get set of all ancestors of set of terms
get.case.based.colours | Function to set colours of HPO nodes in plot to distinguish terms belonging to different sets of phenotypes
get.case.based.labels | Function to label HPO nodes in plot to indicate to which phenotypes each of the terms belong
get.case.term.matrix | Get a matrix with columns of hpo terms and rows of patients,
get.code.node.labels | Function to label HPO nodes in plot with just HPO code
get.descendants | Get set of all descendants of single term
get.frequency.based.colours | Function to colour HPO nodes in plot with colours based on frequency with which terms appear in phenotypes
get.frequency.based.labels | Function to label HPO nodes in plot based on frequency of occurrence in phenotypes
get.frequency.based.sizes | Function to size HPO nodes in plot based on frequency of occurrence in phenotypes
get.full.labels | Function to label HPO nodes in plot with full labels
get.hpo.graph | Get HPO graph object
get.informative.node.labels | Function to label HPO nodes in plot with node description and information content
get.mpo.to.hpo | Get MPO to HPO R-Object
get.node.friendly.long.names | Split up the HPO term descriptions so they fit in nodes for plot
get.ontology | Get R-Object representation of ontology from obo file
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
get.shortened.names | Get human readable, shortened (where possible) HPO term names
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.simple.node.labels | Function to label HPO nodes in plot with just node description
get.term.adjacency.matrix | Get an adjacency for set of HPO terms
get.term.descendancy.matrix | Get logical descendancy matrix for set of terms
get.term.frequencies | Get frequency of each term in a set of phenotypes
get.term.info.content | Get information content of each term in a set of phenotypes
get.term.pseudo.adjacency.matrix | Get an adjacency to MRCA matrix for set of HPO terms
hpo.plot | Plot HPO graph object
hpo.terms | HPO Terms object (based on version 887 of the HPO)
intersection.with.branches | Intersect set of terms with branches of HPO
mpo.terms | MPO Terms object
mpo.to.hpo | Object containing data for mapping between MPO and HPO
n.most.frequent.terms | Select most frequently annotated terms from a set of phenotypes
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
prune.branch | Prune all terms descending from given term down to that term and ensure no degeneracy
remove.links | Remove terms with exactly one parent and child from plot
remove.non.pa.terms | Remove terms not descending from phenotypic abnormality
remove.terms.with.less.than.n.occurrences | Remove terms with less than certain number of occurrences
remove.uninformative.for.plot | Remove uninformative terms (fitting plotting filter format)
remove.uninformative.terms | Get a minimal set of terms which can be used to partition a set of phenotypes
setDimNames | setNames for arrays...
simpleCap | Capitalise words in character vector
swap.out.alt.ids | Remove alternate/deprecated HPO term IDs and swap for new ones
term.set.list.from.character | Get list of character vector of HPO terms, given character vector of comma separated terms