plotQLDisp
From edgeR v3.14.0
by Yunshun Chen
Plot the quasi-likelihood dispersion
Plot the genewise quasi-likelihood dispersion against the gene abundance (in log2 counts per million).
- Keywords
- plot
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 byglmQLFit
. - 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.
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)
Community examples
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