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ontologyPlot (version 1.0)
Functions for Visualising Sets of Ontological Terms
Description
Functions for visualising sets of ontological terms using the graphviz layout system.
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Install
install.packages('ontologyPlot')
Monthly Downloads
470
Version
1.0
License
GPL (>= 2)
Maintainer
Daniel Greene
Last Published
January 11th, 2016
Functions in ontologyPlot (1.0)
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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