Man pages for ontologyPlot
Functions for Visualising Sets of Ontological Terms

annotation_gridGet logical matrix of term annotation for group of cases
calibrate_sizesFunction to scale values between two given limits
colour_by_frequencyFunction to assign colours to terms based on frequency with...
colour_by_population_frequencyFunction to assign colours to terms based on population...
colour_by_term_setFunction to set colours of nodes in plot to distinguish terms...
dot_string'ontology_plot' object to dot string
get_adjacency_matrixGet an adjacency matrix for a set of ontological terms
get_node_friendly_long_namesSplit up node labels across lines so they fit in nodes better
get_ontology_plotGet 'ontology_plot' object
get_pseudo_adjacency_matrixGet an adjacency matrix for a set of ontological terms
get_shortened_namesGet human readable, shortened (where possible) ontological...
grid_termsGet set of HPO terms appropriate for showing in a grid
label_by_frequencyFunction to get plot labels for terms based on frequency in...
label_by_term_setFunction to label nodes by 'term_set'
long_labelsFunction to assign detailed node labels to terms
n_most_frequent_termsSelect 'n' most prevalent terms in 'term_sets'
official_labelsGet official names for terms
ontologyPlot-packageFunctions for Visualising Sets of Ontological Terms
onto_plotGet 'ontology_plot' object
plot_annotation_gridPlot a logical matrix of term annotation
plot.ontology_plotPlotting function for 'ontology_plot' object
print.ontology_plotPrint function for 'ontology_plot' object
p_values_for_occurrence_of_term_in_groupGet p-values for observing at least as many of each term as...
remove_linksRemove terms which just link two other terms together in a...
remove_terms_with_less_than_n_occurrencesRemove terms with less than certain number of occurrences
remove_uninformative_termsRemove uninformative terms from union of all terms in set of...
simple_capCapitalise words in character vector
simple_labelsGet simplified labels for terms
to_svg_stringConvert 'ontology_plot' to SVG string
width_by_frequencyFunction to get node sizes for terms based on frequency in...
width_by_significanceFunction to get node sizes for terms based on statistical...
write_dotExport 'ontology_plot' object as dot file
ontologyPlot documentation built on May 29, 2017, 5:52 p.m.