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Last data update: 2014.03.03

R: Plot Biological Coefficient of Variation

plotBCV

R Documentation

Plot Biological Coefficient of Variation

Description

Plot the genewise biological coefficient of variation (BCV) against gene abundance (in log2 counts per million).

Usage

plotBCV(y, xlab="Average log CPM", ylab="Biological coefficient of variation",
     pch=16, cex=0.2, col.common="red", col.trend="blue", col.tagwise="black", ...)

Arguments

`y`	a `DGEList` object.
`xlab`	label for the x-axis.
`ylab`	label for the y-axis.
`pch`	the plotting symbol. See `points` for more details.
`cex`	plot symbol expansion factor. See `points` for more details.
`col.common`	color of line showing common dispersion
`col.trend`	color of line showing dispersion trend
`col.tagwise`	color of points showing genewise dispersions. Note that ‘tag’ and ‘gene’ are synonymous here.
`...`	any other arguments are passed to `plot`.

Details

The BCV is the square root of the negative binomial dispersion. This function displays the common, trended and genewise BCV estimates.

Value

A plot is created on the current graphics device.

Author(s)

Davis McCarthy, Yunshun Chen, Gordon Smyth

Examples

BCV.true <- 0.1
y <- DGEList(matrix(rnbinom(6000, size = 1/BCV.true^2, mu = 10),1000,6))
y <- estimateCommonDisp(y)
y <- estimateTrendedDisp(y)
y <- estimateTagwiseDisp(y)
plotBCV(y)

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(edgeR)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/edgeR/plotBCV.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBCV
> ### Title: Plot Biological Coefficient of Variation
> ### Aliases: plotBCV
> ### Keywords: plot
> 
> ### ** Examples
> 
> BCV.true <- 0.1
> y <- DGEList(matrix(rnbinom(6000, size = 1/BCV.true^2, mu = 10),1000,6))
> y <- estimateCommonDisp(y)
> y <- estimateTrendedDisp(y)
> y <- estimateTagwiseDisp(y)
> plotBCV(y)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>