R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plot the quasi-likelihood dispersion

plotQLDisp

R Documentation

Plot the quasi-likelihood dispersion

Description

Plot the genewise quasi-likelihood dispersion against the gene abundance (in log2 counts per million).

Usage

plotQLDisp(glmfit, xlab="Average Log2 CPM", ylab="Quarter-Root Mean Deviance", pch=16, 
       cex=0.2, col.shrunk="red", col.trend="blue", col.raw="black", ...)

Arguments

`glmfit`	a `DGEGLM` object produced by `glmQLFit`.
`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.shrunk`	color of the points representing the shrunk quasi-liklihood dispersions.
`col.trend`	color of line showing dispersion trend.
`col.raw`	color of points showing the unshrunk dispersions.
`...`	any other arguments are passed to `plot`.

Details

This function displays the quarter-root of the quasi-likelihood dispersions for all genes, before and after shrinkage towards a trend. If glmfit was constructed without an abundance trend, the function instead plots a horizontal line (of colour col.trend) at the common value towards which dispersions are shrunk. The quarter-root transformation is applied to improve visibility for dispersions around unity.

Value

A plot is created on the current graphics device.

Author(s)

Aaron Lun, based on code by Davis McCarthy and Gordon Smyth

Examples

nbdisp <- 1/rchisq(1000, df=10)
y <- DGEList(matrix(rnbinom(6000, size = 1/nbdisp, mu = 10),1000,6))
design <- model.matrix(~factor(c(1,1,1,2,2,2)))
y <- estimateDisp(y, design)

fit <- glmQLFit(y, design)
plotQLDisp(fit)

fit <- glmQLFit(y, design, abundance.trend=FALSE)
plotQLDisp(fit)

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/plotQLDisp.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotQLDisp
> ### Title: Plot the quasi-likelihood dispersion
> ### Aliases: plotQLDisp
> ### Keywords: plot
> 
> ### ** Examples
> 
> nbdisp <- 1/rchisq(1000, df=10)
> y <- DGEList(matrix(rnbinom(6000, size = 1/nbdisp, mu = 10),1000,6))
> design <- model.matrix(~factor(c(1,1,1,2,2,2)))
> y <- estimateDisp(y, design)
> 
> fit <- glmQLFit(y, design)
> plotQLDisp(fit)
> 
> fit <- glmQLFit(y, design, abundance.trend=FALSE)
> plotQLDisp(fit)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>