genomation (version 1.4.2)

plotGeneAnnotation: Plots the enrichment of each feature in the set in the gene annotation

Description

This function plots a heatmap of enrichment of each range in given gene feature

Usage

plotGeneAnnotation(l, cluster = FALSE, col = c("white", "cornflowerblue"))
## S3 method for class 'list':
plotGeneAnnotation(l, cluster = FALSE, col = c("white",
  "cornflowerblue"))

Arguments

l

a list of AnnotationByGeneParts objects

cluster

TRUE/FALSE. If TRUE the heatmap is going to be clustered using hierarchical clustering

col

a vector of two colors that will be used for interpolation. The first color is the lowest one, the second is the highest one

Value

• plots a heatmap of enrichment of target in each gene functional category

Examples

library(GenomicRanges)
data(cage)
data(cpgi)

cage$tpm = NULL
gl = GRangesList(cage=cage, cpgi=cpgi)

bed.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
gene.parts = readTranscriptFeatures(bed.file)
annot = annotateWithGeneParts(gl, gene.parts, intersect.chr=TRUE)
plotGeneAnnotation(annot)