Package: rrvgo 1.19.0

Sergi Sayols

rrvgo: Reduce + Visualize GO

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Authors:Sergi Sayols [aut, cre], Sara Elmeligy [ctb]

# Install 'rrvgo' in R:

install.packages('rrvgo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:rrvgo-1.19.0(bioc 3.21)rrvgo-1.18.0(bioc 3.20)

Last updated 2 months agofrom:b7ae543824. Checks:OK: 1 NOTE: 6. Indexed: yes.

Sergi Sayols

Last update: 2023-10-17
Started: 2020-02-27

Help page	Topics
calculateSimMatrix Calculate the score similarity matrix between terms	calculateSimMatrix
getGoSize Get GO term size (# of genes)	getGoSize
getGoTerm Get the description of a GO term	getGoTerm
getTermDisp Calculate the term dispensability score, defined as the semantic similarity threshold a term was assigned to a cluster (namely, the similarity of a term to the cluster representative term).	getTermDisp
getTermUniq Calculate the term uniqueness score, defined as 1 minus the average semantic similarity of a term to all other terms.	getTermUniq
gg_color_hue Emulate ggplot2 color palette.	gg_color_hue
heatmapPlot Plot similarity matrix as a heatmap	heatmapPlot
loadOrgdb Load an orgdb object	loadOrgdb
reduceSimMatrix Reduce a set of GO terms based on their semantic similarity and scores.	reduceSimMatrix
scatterPlot Plot GO terms as scattered points.	scatterPlot
shiny_rrvgo Launch an interactive web interface.	shiny_rrvgo
treemapPlot Plot GO terms as a treemap.	treemapPlot
wordlcoudPlot Plot GO reduced terms as a wordcloud.	wordcloudPlot