                        Functions for Plotting HPO Terms
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.grey.borders        Function to border HPO nodes in plot with grey
                        borders
get.hpo.graph           Get HPO graph object
get.hpo.terms           Gets HPO R-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.no.borders          Function to border HPO nodes in plot with
                        transparent borders
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.standard.sizes      Function to size HPO nodes in plot 0.75 inches
                        across
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
get.white.nodes         Function to colour HPO nodes in plot white
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
