It is so easy to plot data using R that I don't see any need for limma to provide wrapper functions for everything. For example, if
y is an
EList object in limma,
Group is a factor, and you want to plot gene
i vs Group, then just
boxplot(y$E[i,] ~ Group)
y is a different type of object, then just substitute
exprs(y) is the matrix of log-expression values.
You seem to be assuming that you can plot data from the linear model fit, but you can't. The expresssion data is stored in the data object not in the fit object.
Your question might be partly about how to set
i, but you would need to give more information about your code pipeline for people to help you with that.
The reference to
plotCounts is a bit confusing since it doesn't make boxplots and doesn't work with contrasts.