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 |

**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

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
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