R: Plot feature performance of a TargetExperiment object.
plotAttrPerform
R Documentation
Plot feature performance of a TargetExperiment object.
Description
plotAttrPerform plots the achieved performance for the selected
attribute. The resulting graph shows one bar per each attribute interval and
its height is defined according to the amount of features achieving attribute
values within that interval.
## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")
# Definition of the interval extreme values
attributeThres<-c(0,1,50,200,500, Inf)
# Plot panel overview in a feature performance plot
g<-plotAttrPerform(ampliPanel, attributeThres=attributeThres)
if(interactive()){
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-plotAttrPerform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAttrPerform
> ### Title: Plot feature performance of a TargetExperiment object.
> ### Aliases: plotAttrPerform plotAttrPerform,TargetExperiment-method
> ### plotAttrPerform-methods
>
> ### ** Examples
>
> ## Loading the TargetExperiment object
> data(ampliPanel, package="TarSeqQC")
>
> # Definition of the interval extreme values
> attributeThres<-c(0,1,50,200,500, Inf)
>
> # Plot panel overview in a feature performance plot
> g<-plotAttrPerform(ampliPanel, attributeThres=attributeThres)
> #if(interactive()){
> g
> #}
>
>
>
>
>
> dev.off()
null device
1
>