ontologyPlot: Functions for Visualising Sets of Ontological Terms

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

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

Files

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

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

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