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"))

## S4 method for signature 'list'
plotGeneAnnotation(l, cluster = FALSE, col = c("white",
  "cornflowerblue"))

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(genomation)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genomation/plotGeneAnnotation-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGeneAnnotation
> ### Title: Plots the enrichment of each feature in the set in the gene
> ###   annotation
> ### Aliases: plotGeneAnnotation
> ###   plotGeneAnnotation,AnnotationByFeature-method
> ###   plotGeneAnnotation,list-method
> 
> ### ** Examples
> 
> library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 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)
Reading the table... 
Calculating intron coordinates... 
Calculating exon coordinates... 
Calculating TSS coordinates... 
Calculating promoter coordinates... 
Outputting the final GRangesList... 

> annot = annotateWithGeneParts(gl, gene.parts, intersect.chr=TRUE)
Working on: cage
intersecting chromosomes...
Working on: cpgi
intersecting chromosomes...
> ## No test: 
> plotGeneAnnotation(annot)
> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>