⚠️There's a newer version (1.7) of this package.Take me there.

ontologyPlot (version 1.0)

Functions for Visualising Sets of Ontological Terms

Description

Functions for visualising sets of ontological terms using the graphviz layout system.

Copy Link

Version

Install

install.packages('ontologyPlot')

Monthly Downloads

469

Version

1.0

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

January 11th, 2016

Functions in ontologyPlot (1.0)

ontologyPlot

Functions for Visualising Sets of Ontological Terms

long_labels

Function to assign detailed node labels to terms

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

plot.ontology_plot

Plotting function for ontology_plot object

onto_plot

Get ontology_plot object

get_shortened_names

Get human readable, shortened (where possible) ontological term names

n_most_frequent_terms

Select n most prevalent terms in term_sets

label_by_frequency

Function to get plot labels for terms based on frequency in term_sets

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

simple_cap

Capitalise words in character vector

calibrate_sizes

Function to scale values between two given limits

only_phenotype_abnormalities

Remove terms not descending from phenotypic abnormality

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

label_by_term_set

Function to label nodes by term_set

simple_labels

Get simplified labels for terms

remove_terms_with_less_than_n_occurrences

Remove terms with less than certain number of occurrences

write_dot

Function to write dot file

colour_by_frequency

Function to assign colours to terms based on frequency with which terms appear 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

official_labels

Get official names for terms

remove_uninformative_terms

Retain only the most specific terms which are present in each unique set of term sets

width_by_frequency

Function to get node sizes for terms based on frequency in term_sets

print.ontology_plot

Print function for ontology_plot object

get_pseudo_adjacency_matrix

Get an adjacency matrix for a set of ontological terms

remove_links

Remove terms which just link two other terms