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Last data update: 2014.03.03

R: Plot TargetExperiment object overview.

plot	R Documentation

Plot TargetExperiment object overview.

Description

plot allows a fast and simple representation of one feature panel using a polar histogram plot. Histogram bar reflects the percentage of features that have shown the analyzed attribute in a user setted interval. The resulting graph can be busy and might be better off saved.

Usage

## S4 method for signature 'TargetExperiment,ANY'
plot(x, y, attributeThres = c(0, 1, 50, 200,
    500, Inf), binSize = 1, spaceGene = 0.2, spaceChr = 1.2,
    innerRadius = 0.3, outerRadius = 1, guides = c(20, 40, 60, 80),
    alphaStart = -0.3, circleProportion = 0.95, direction = "inwards",
    chrLabels = FALSE)

Arguments

`x`	TargetExperiment class object.
`y`	not used but necessary for redefining the generic function.
`attributeThres`	Numeric indicating the interval extreme values.
`binSize`	Numeric indicating bin width. Should probably be left as 1, as other parameters are relative to it.
`spaceGene`	Numeric. Space between bins.
`spaceChr`	Numeric. Space between chromosomes.
`innerRadius`	Numeric. Radius of inner circle.
`outerRadius`	Numeric. Radius of outer circle.
`guides`	A vector with percentages to use for the white guide lines.
`alphaStart`	Numeric offset from 12 o'clock in radians.
`circleProportion`	Numeric proportion of the circle to cover.
`direction`	Character indicating if the increasing count goes from or to the centre.
`chrLabels`	Logical. Chromosome names must be plotted?.

Value

a ggplot2 graph.

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

References

http://www.r-bloggers.com/polar-histogram-pretty-and-useful/

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
g<-plot(ampliPanel, attributeThres, chrLabels =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)

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-plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot
> ### Title: Plot TargetExperiment object overview.
> ### Aliases: plot plot,TargetExperiment,ANY-method
> 
> ### ** 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
> g<-plot(ampliPanel, attributeThres, chrLabels =TRUE)
> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>