heatmapPlot: heatmapPlot Plot similarity matrix as a heatmap

In ssayols/RVGO: Reduce + Visualize GO

heatmapPlot Plot similarity matrix as a heatmap

Description

heatmapPlot Plot similarity matrix as a heatmap

Usage

heatmapPlot(
  simMatrix,
  reducedTerms = NULL,
  annotateParent = TRUE,
  annotationLabel = "parentTerm",
  ...
)

Arguments

simMatrix	a (square) similarity matrix.
reducedTerms	a data.frame with the reduced terms from reduceSimMatrix()
annotateParent	whether to add annotation of the parent
annotationLabel	display "parent" ids or "parentTerm" string
...	other parameters sent to pheatmap::pheatmap()

Details

Matrix with similarity scores between terms is represented as a heatmap.

Value

Invisibly a pheatmap object that is a list with components

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")
heatmapPlot(simMatrix, reducedTerms, annotateParent=TRUE, annotationLabel="parentTerm", fontsize=6)

ssayols/RVGO documentation built on Oct. 31, 2024, 12:27 p.m.