heatmapPlot: heatmapPlot Plot similarity matrix as a heatmap

Description Usage Arguments Details Value Examples

View source: R/plotlib.R

Description

heatmapPlot Plot similarity matrix as a heatmap

Usage

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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

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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/rrvgo-ci documentation built on March 17, 2020, 12:14 a.m.