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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
1.7
1.6
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1.3
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Install
install.packages('ontologyPlot')
Monthly Downloads
383
Version
1.7
License
GPL (>= 2)
Maintainer
Daniel Greene
Last Published
February 20th, 2024
Functions in ontologyPlot (1.7)
Search functions
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