volcanoplot {limma} | R Documentation |
Creates a volcano plot for a specified coefficient of a linear model.
volcanoplot(fit, coef = 1L, style = "p-value", highlight = 0, names = fit$genes$ID, xlab = "Log2 Fold Change", ylab = NULL, pch=16, cex=0.35, ...)
fit |
an |
coef |
index indicating which coefficient of the linear model is to be plotted. |
style |
character string indicating which significance statistic to plot on the y-axis. Possibilities are |
highlight |
number of top genes to be highlighted by name. |
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 |
A volcano plot displays log fold changes on the x-axis versus a measure of statistical significance on the y-axis. Here the significance measure can be -log(p-value) or the B-statistics, which give the posterior log-odds of differential expression.
The plot is optionally annotated with the names of the most significant genes.
No value is returned but 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