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 |