Plot read profiles for a particular genomic region.

Description

plotRegion plots the read profiles for a selected region. If SNPs is set as 'TRUE', colored bars will appear indicating the ocurrence of SNPs at each genomic position.

Usage

plotRegion(object, region, seqname, SNPs = TRUE, xlab = "", title = "",
    size = 0.5, BPPARAM = bpparam())

## S4 method for signature 'TargetExperiment'
plotRegion(object, region, seqname, SNPs = TRUE,
    xlab = "", title = "", size = 0.5, BPPARAM = bpparam())

Arguments

Value

ggplot2 graphics.

include TargetExperiment-FeatPerform.R

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

See Also

plotFeature

Examples

if(interactive()){
## loading TargetExperiment object
data(ampliPanel, package="TarSeqQC")
## Defining bam file, bed file and fasta file names and paths
setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
    package="TarSeqQC", mustWork=TRUE)
setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
    package="TarSeqQC", mustWork=TRUE)

# getting and exploring a sequenced region of a particular gene
getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
# plot a particular genomic region
g<-plotRegion(ampliPanel,region=c(4500,6800), seqname="chr10", SNPs=TRUE,
xlab="", title="gene7 amplicons",size=0.5)
# x11(type="cairo")
g
}

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(TarSeqQC)
Loading required package: 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
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-plotRegion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRegion
> ### Title: Plot read profiles for a particular genomic region.
> ### Aliases: plotRegion plotRegion,TargetExperiment-method
> ###   plotRegion-methods
> 
> ### ** Examples
> 
> #if(interactive()){
> ## loading TargetExperiment object
> data(ampliPanel, package="TarSeqQC")
> ## Defining bam file, bed file and fasta file names and paths
> setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
+     package="TarSeqQC", mustWork=TRUE)
> setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
+     package="TarSeqQC", mustWork=TRUE)
> 
> # getting and exploring a sequenced region of a particular gene
> getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
   names seqname start  end  gene
1 AMPL18   chr10   141  233 gene7
2 AMPL19   chr10  1007 1079 gene7
3 AMPL20   chr10  4866 4928 gene7
4 AMPL21   chr10  6632 6693 gene7
5 AMPL22   chr10  8475 8527 gene7
> # plot a particular genomic region
> g<-plotRegion(ampliPanel,region=c(4500,6800), seqname="chr10", SNPs=TRUE,
+ xlab="", title="gene7 amplicons",size=0.5)
> # x11(type="cairo")
> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>