Man pages for ontologyPlot
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... |
| colour_by_population_frequency | Function to assign colours to terms based on population... |
| colour_by_term_set | Function to set colours of nodes in plot to distinguish terms... |
| 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... |
| 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... |
| 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-package | Functions for Visualising Sets of Ontological Terms |
| onto_plot | Get 'ontology_plot' object |
| plot_annotation_grid | Plot a logical matrix of term annotation |
| 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... |
| remove_links | Remove terms which just link two other terms together in a... |
| 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... |
| 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... |
| width_by_significance | Function to get node sizes for terms based on statistical... |
| write_dot | Export 'ontology_plot' object as dot file |
