Plot the attribute value for all the features of a selected gene.

Description

plotGeneAttrPerFeat plots the achieved performance for each feature for a particular gene. The resulting graph shows one bar per each gene feature with heights according to its attribute value.

Usage

plotGeneAttrPerFeat(object, geneID)

## S4 method for signature 'TargetExperiment'
plotGeneAttrPerFeat(object, geneID)

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

plotAttrExpl

Examples

if(interactive()){
## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")

# Exploring amplicon attribute values for a particular gene
g<-plotGeneAttrPerFeat(ampliPanel, geneID="gene4")
# Adjust text size
g<-g+theme(title=element_text(size=16), axis.title=element_text(size=16),
legend.text=element_text(size=14))
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-plotGeneAttrPerFeat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGeneAttrPerFeat
> ### Title: Plot the attribute value for all the features of a selected
> ###   gene.
> ### Aliases: plotGeneAttrPerFeat
> ###   plotGeneAttrPerFeat,TargetExperiment-method
> ###   plotGeneAttrPerFeat-methods
> 
> ### ** Examples
> 
> #if(interactive()){
> ## Loading the TargetExperiment object
> data(ampliPanel, package="TarSeqQC")
> 
> # Exploring amplicon attribute values for a particular gene
> g<-plotGeneAttrPerFeat(ampliPanel, geneID="gene4")
> # Adjust text size
> g<-g+theme(title=element_text(size=16), axis.title=element_text(size=16),
+ legend.text=element_text(size=14))
> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>