Functions for visualising sets of ontological terms using the 'graphviz' layout system.
|Author||Daniel Greene <email@example.com>|
|Date of publication||2016-10-28 01:13:50|
|Maintainer||Daniel Greene <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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