ontologyPlot: Functions for Visualising Sets of Ontological Terms

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

Author
Daniel Greene <dg333@cam.ac.uk>
Date of publication
2016-10-28 01:13:50
Maintainer
Daniel Greene <dg333@cam.ac.uk>
License
GPL (>= 2)
Version
1.4

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

Files in this package

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