ontologyPlot: Functions for Visualising Sets of Ontological Terms
Version 1.4

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

Browse man pages Browse package API and functions Browse package files

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

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

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

Files

inst
inst/doc
inst/doc/plotting-term-grids.Rmd
inst/doc/plotting-term-grids.html
inst/doc/plotting-ontological-terms.Rmd
inst/doc/plotting-ontological-terms.R
inst/doc/plotting-ontological-terms.html
inst/doc/plotting-term-grids.R
NAMESPACE
R
R/attributes.R
R/sets.R
R/graphs.R
R/data.R
R/annotation_grid.R
vignettes
vignettes/plotting-term-grids.Rmd
vignettes/plotting-ontological-terms.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/simple_cap.Rd
man/print.ontology_plot.Rd
man/to_svg_string.Rd
man/remove_terms_with_less_than_n_occurrences.Rd
man/colour_by_population_frequency.Rd
man/remove_links.Rd
man/official_labels.Rd
man/n_most_frequent_terms.Rd
man/label_by_frequency.Rd
man/ontologyPlot-package.Rd
man/get_shortened_names.Rd
man/plot.ontology_plot.Rd
man/get_adjacency_matrix.Rd
man/dot_string.Rd
man/get_ontology_plot.Rd
man/grid_terms.Rd
man/p_values_for_occurrence_of_term_in_group.Rd
man/long_labels.Rd
man/onto_plot.Rd
man/colour_by_frequency.Rd
man/label_by_term_set.Rd
man/width_by_frequency.Rd
man/remove_uninformative_terms.Rd
man/plot_annotation_grid.Rd
man/get_pseudo_adjacency_matrix.Rd
man/simple_labels.Rd
man/write_dot.Rd
man/annotation_grid.Rd
man/get_node_friendly_long_names.Rd
man/colour_by_term_set.Rd
man/calibrate_sizes.Rd
man/width_by_significance.Rd
ontologyPlot documentation built on May 19, 2017, 3:42 p.m.