Plot read profiles for a particular feature.

Description

plotFeature plots the achieved performance for each feature/gene. The resulting graph shows one bar per each feature/gene with heights according to its attribute value. If complete is set as TRUE two bar plots (feature and gene level) will be stored in the resulting ggplot object.

Usage

plotFeature(object, featureID, SNPs = TRUE, xlab = "", title = "",
    size = 0.5, BPPARAM = bpparam())

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

Arguments

Value

ggplot2 graphics.

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

plotRegion

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)

# Exploring the read count profile for a particular amplicon
g<-plotFeature(ampliPanel, featureID="AMPL20")
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.

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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-plotFeature.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotFeature
> ### Title: Plot read profiles for a particular feature.
> ### Aliases: plotFeature plotFeature,TargetExperiment-method
> ###   plotFeature-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)
> 
> # Exploring the read count profile for a particular amplicon
> g<-plotFeature(ampliPanel, featureID="AMPL20")
   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%

   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%

> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>