It is easy to produce figures with multiple panels in R.

For example for four panels:

par(mfrow=c(2,2))

Every new plot call, will add a plot to the next panel in the 2 by 2 table generated. Once all panels are filled, they are erased and the plots are added from the beginning.

It is not easy to label each panel.

One way is to add text in a specific non-standard place:

mtext("A", side=3, line=1, adj=0, font=2, cex=2)

This is nice as the text is added automatically and is always in the same relative location in the different panels.

A more flexible way is to add text after clicking on the graph. However this is a manual process:

par(mfrow=c(1,2)) 
plot(x~y) 
text(locator(1),"A") 
plot(x~z) 
text(locator(1),"B")

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