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... |

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 |

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