R: Visualising Sets of Ontological Terms

# 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