Functions for Visualising Sets of Ontological Terms


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Documentation for package ‘ontologyPlot’ version 1.0

Help Pages

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
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_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
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
only_phenotype_abnormalities Remove terms not descending from phenotypic abnormality
onto_plot Get ontology_plot object
plot.ontology_plot Plotting function for 'ontology_plot' object
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
remove_terms_with_less_than_n_occurrences Remove terms with less than certain number of occurrences
remove_uninformative_terms Retain only the most specific terms which are present in each unique set of term sets
simple_cap Capitalise words in character vector
simple_labels Get simplified labels for terms
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 Function to write dot file