| volcanoplot {limma} | R Documentation |
Creates a volcano plot of log-fold changes versus log-odds of differential expression.
volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, xlab="Log Fold Change", ylab="Log Odds", pch=16, cex=0.35, ...)
fit |
an MArrayLM fitted linear model object |
coef |
integer giving the coefficient |
highlight |
number of top genes to be highlighted |
names |
character vector giving text labels for the probes to be used in highlighting |
xlab |
character string giving label for x-axis |
ylab |
character string giving label for y-axis |
pch |
vector or list of plotting characters. Default is integer code 16 which gives a solid circle. |
cex |
numeric vector of plot symbol expansions. Default is 0.35. |
... |
any other arguments are passed to plot |
A volcano plot is any plot which displays fold changes versus a measure of statistical significance of the change.
A plot is created on the current graphics device.
Gordon Smyth
An overview of presentation plots following the fitting of a linear model in LIMMA is given in 06.LinearModels.
# See lmFit examples