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ontologyPlot (version 1.7)

Visualising Sets of Ontological Terms

Description

Create R plots visualising ontological terms and the relationships between them with various graphical options - Greene et al. 2017 .

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Version

Install

install.packages('ontologyPlot')

Monthly Downloads

469

Version

1.7

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

February 20th, 2024

Functions in ontologyPlot (1.7)

plot.ontology_plot

Plotting function for ontology_plot object
remove_terms_with_less_than_n_occurrences

Remove terms with less than certain number of occurrences
long_labels

Function to assign detailed node labels to terms
print.ontology_plot

Print function for ontology_plot object
remove_links

Remove terms which just link two other terms together in a subontology
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
width_by_frequency

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

Select n most prevalent terms in term_sets
to_svg_string

Convert ontology_plot to SVG string
plot_annotation_grid

Plot a logical matrix of term annotation
remove_uninformative_terms

Remove uninformative terms from union of all terms in set of annotations
simple_labels

Get simplified labels for terms
write_dot

Export ontology_plot object as dot file
simple_cap

Capitalise words in character vector
calibrate_sizes

Function to scale values between two given limits
get_adjacency_matrix

Get an adjacency matrix for a set of ontological terms
colour_by_frequency

Function to assign colours to terms based on frequency with which terms appear in term_sets
annotation_grid

Get logical matrix of term annotation for group of cases
dot_string

ontology_plot object to dot string
get_pseudo_adjacency_matrix

Get an adjacency matrix for a set of ontological terms
colour_by_term_set

Function to set colours of nodes in plot to distinguish terms belonging to different term sets
colour_by_population_frequency

Function to assign colours to terms based on population frequency of 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
ontologyPlot

Functions for Visualising Sets of Ontological Terms
label_by_frequency

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

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

Get official names for terms
grid_terms

Get set of HPO terms appropriate for showing in a grid
label_by_term_set

Function to label nodes by term_set
onto_plot

Get ontology_plot object
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