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 |