ontologyPlot: Functions for Visualising Sets of Ontological Terms

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

Install the latest version of this package by entering the following in R:
install.packages("ontologyPlot")
AuthorDaniel Greene <dg333@cam.ac.uk>
Date of publication2016-10-28 01:13:50
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version1.4

View on CRAN

Man pages

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

Functions

annotation_grid Man page
calibrate_sizes Man page
colour_by_frequency Man page
colour_by_population_frequency Man page
colour_by_term_set Man page
dot_string Man page
get_adjacency_matrix Man page
get_node_friendly_long_names Man page
get_ontology_plot Man page
get_pseudo_adjacency_matrix Man page
get_shortened_names Man page
grid_terms Man page
label_by_frequency Man page
label_by_term_set Man page
long_labels Man page
n_most_frequent_terms Man page
official_labels Man page
onto_plot Man page
plot_annotation_grid Man page
plot.ontology_plot Man page
print.ontology_plot Man page
p_values_for_occurrence_of_term_in_group Man page
remove_links Man page
remove_terms_with_less_than_n_occurrences Man page
remove_uninformative_terms Man page
simple_cap Man page
simple_labels Man page
to_svg_string Man page
width_by_frequency Man page
width_by_significance Man page
write_dot Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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