Plot feature performance of a TargetExperiment object.

Description

plotFeatPerform plots the achieved performance for each feature/gene. The resulting graph shows one bar per each feature/gene with height 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

plotFeatPerform(object, attributeThres = c(0, 1, 50, 200, 500, Inf),
    complete = TRUE, log = TRUE, featureLabs = FALSE, sepChr = FALSE,
    legend = TRUE)

## S4 method for signature 'TargetExperiment'
plotFeatPerform(object, attributeThres = c(0, 1,
    50, 200, 500, Inf), complete = TRUE, log = TRUE, featureLabs = FALSE,
    sepChr = FALSE, legend = TRUE)

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

plot

Examples

if(interactive()){
## 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<-plotFeatPerform(ampliPanel, attributeThres=attributeThres, log=FALSE,
featureLabs=TRUE, sepChr=TRUE, legend=TRUE)
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)

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'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-plotFeatPerform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotFeatPerform
> ### Title: Plot feature performance of a TargetExperiment object.
> ### Aliases: plotFeatPerform plotFeatPerform,TargetExperiment-method
> ###   plotFeatPerform-methods
> 
> ### ** Examples
> 
> #if(interactive()){
> ## 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<-plotFeatPerform(ampliPanel, attributeThres=attributeThres, log=FALSE,
+ featureLabs=TRUE, sepChr=TRUE, legend=TRUE)
Error: stat_bin() must not be used with a y aesthetic.
In addition: Warning messages:
1: `geom_bar()` no longer has a `binwidth` parameter. Please use `geom_histogram()` instead. 
2: `show_guide` has been deprecated. Please use `show.legend` instead. 
Execution halted