Visualising Sets of Ontological Terms

---

Documentation for package ‘ontologyPlot’ version 1.7

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

Help Pages

ontologyPlot-package	Functions for Visualising Sets of Ontological Terms
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
ontologyPlot	Functions for Visualising Sets of Ontological Terms
onto_plot	Get 'ontology_plot' object
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
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
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