Package: ontologyPlot 1.7

ontologyPlot: Visualising Sets of Ontological Terms

Create R plots visualising ontological terms and the relationships between them with various graphical options - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.

Authors:Daniel Greene <[email protected]>

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ontologyPlot.pdf |ontologyPlot.html✨
ontologyPlot/json (API)

# Install 'ontologyPlot' in R:
install.packages('ontologyPlot', repos = c('https://daniel-jg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.26 score 3 packages 51 scripts 354 downloads 2 mentions 27 exports 5 dependencies

Last updated 9 months agofrom:c0744042db. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winOKOct 18 2024
R-4.5-linuxOKOct 18 2024
R-4.4-winOKOct 18 2024
R-4.4-macOKOct 18 2024
R-4.3-winOKOct 18 2024
R-4.3-macOKOct 18 2024

Exports:annotation_gridcalibrate_sizescolour_by_frequencycolour_by_population_frequencycolour_by_term_setdot_stringget_adjacency_matrixget_node_friendly_long_namesget_pseudo_adjacency_matrixget_shortened_namesgrid_termslabel_by_frequencylabel_by_term_setlong_labelsn_most_frequent_termsofficial_labelsonto_plotp_values_for_occurrence_of_term_in_groupplot_annotation_gridremove_linksremove_terms_with_less_than_n_occurrencesremove_uninformative_termssimple_capsimple_labelswidth_by_frequencywidth_by_significancewrite_dot

Dependencies:BiocGenericsgraphontologyIndexpaintmapRgraphviz

Plotting Ontological Terms

Daniel Greene

Rendered fromplotting-ontological-terms.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-02-21
Started: 2016-09-09

Plotting Term Grids

Daniel Greene

Rendered fromplotting-term-grids.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-02-21
Started: 2016-09-09

Readme and manuals

Help Manual

Help pageTopics
Get logical matrix of term annotation for group of casesannotation_grid
Function to scale values between two given limitscalibrate_sizes
Function to assign colours to terms based on frequency with which terms appear in 'term_sets'colour_by_frequency
Function to assign colours to terms based on population frequency of termscolour_by_population_frequency
Function to set colours of nodes in plot to distinguish terms belonging to different term setscolour_by_term_set
'ontology_plot' object to dot stringdot_string
Get an adjacency matrix for a set of ontological termsget_adjacency_matrix
Split up node labels across lines so they fit in nodes betterget_node_friendly_long_names
Get 'ontology_plot' objectget_ontology_plot
Get an adjacency matrix for a set of ontological termsget_pseudo_adjacency_matrix
Get human readable, shortened (where possible) ontological term namesget_shortened_names
Get set of HPO terms appropriate for showing in a gridgrid_terms
Function to get plot labels for terms based on frequency in 'term_sets'label_by_frequency
Function to label nodes by 'term_set'label_by_term_set
Function to assign detailed node labels to termslong_labels
Select 'n' most prevalent terms in 'term_sets'n_most_frequent_terms
Get official names for termsofficial_labels
Get 'ontology_plot' objectonto_plot
Functions for Visualising Sets of Ontological TermsontologyPlot-package ontologyPlot
Get p-values for observing at least as many of each term as occur in 'term_sets' given the population frequencies of the termsp_values_for_occurrence_of_term_in_group
Plot a logical matrix of term annotationplot_annotation_grid
Plotting function for 'ontology_plot' objectplot.ontology_plot
Print function for 'ontology_plot' objectprint.ontology_plot
Remove terms which just link two other terms together in a subontologyremove_links
Remove terms with less than certain number of occurrencesremove_terms_with_less_than_n_occurrences
Remove uninformative terms from union of all terms in set of annotationsremove_uninformative_terms
Capitalise words in character vectorsimple_cap
Get simplified labels for termssimple_labels
Convert 'ontology_plot' to SVG stringto_svg_string
Function to get node sizes for terms based on frequency in 'term_sets'width_by_frequency
Function to get node sizes for terms based on statistical significance of seeing at least this number of each term in 'term_sets'width_by_significance
Export 'ontology_plot' object as dot filewrite_dot