wordcloudPlot: wordlcoudPlot Plot GO reduced terms as a wordcloud.

In imbforge/rrvgo: Reduce + Visualize GO

wordlcoudPlot Plot GO reduced terms as a wordcloud.

Description

wordlcoudPlot Plot GO reduced terms as a wordcloud.

Usage

wordcloudPlot(reducedTerms, onlyParents = TRUE, ...)

Arguments

reducedTerms	a data.frame with the reduced terms from reduceSimMatrix().
onlyParents	use only parent terms to calculate frequencies.
...	other parameters sent to wordcloud::wordcloud()

Value

Nothing

Examples

go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo"))
simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel")
scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID)
reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db")
wordcloudPlot(reducedTerms, min.freq=1, colors="black")

imbforge/rrvgo documentation built on Oct. 24, 2024, 12:18 a.m.