annotation_grid         Get logical matrix of term annotation for group
                        of cases
calibrate_sizes         Function to scale values between two given
                        limits
colour_by_frequency     Function to assign colours to terms based on
                        frequency with which terms appear in
                        'term_sets'
colour_by_population_frequency
                        Function to assign colours to terms based on
                        population frequency of terms
colour_by_term_set      Function to set colours of nodes in plot to
                        distinguish terms belonging to different term
                        sets
dot_string              'ontology_plot' object to dot string
get_adjacency_matrix    Get an adjacency matrix for a set of
                        ontological terms
get_node_friendly_long_names
                        Split up node labels across lines so they fit
                        in nodes better
get_ontology_plot       Get 'ontology_plot' object
get_pseudo_adjacency_matrix
                        Get an adjacency matrix for a set of
                        ontological terms
get_shortened_names     Get human readable, shortened (where possible)
                        ontological term names
grid_terms              Get set of HPO terms appropriate for showing in
                        a grid
label_by_frequency      Function to get plot labels for terms based on
                        frequency in 'term_sets'
label_by_term_set       Function to label nodes by 'term_set'
long_labels             Function to assign detailed node labels to
                        terms
n_most_frequent_terms   Select 'n' most prevalent terms in 'term_sets'
official_labels         Get official names for terms
onto_plot               Get 'ontology_plot' object
ontologyPlot            Functions for Visualising Sets of Ontological
                        Terms
p_values_for_occurrence_of_term_in_group
                        Get p-values for observing at least as many of
                        each term as occur in 'term_sets' given the
                        population frequencies of the terms
plot.ontology_plot      Plotting function for 'ontology_plot' object
plot_annotation_grid    Plot a logical matrix of term annotation
print.ontology_plot     Print function for 'ontology_plot' object
remove_links            Remove terms which just link two other terms
                        together in a subontology
remove_terms_with_less_than_n_occurrences
                        Remove terms with less than certain number of
                        occurrences
remove_uninformative_terms
                        Remove uninformative terms from union of all
                        terms in set of annotations
simple_cap              Capitalise words in character vector
simple_labels           Get simplified labels for terms
to_svg_string           Convert 'ontology_plot' to SVG string
width_by_frequency      Function to get node sizes for terms based on
                        frequency in 'term_sets'
width_by_significance   Function to get node sizes for terms based on
                        statistical significance of seeing at least
                        this number of each term in 'term_sets'
write_dot               Export 'ontology_plot' object as dot file
