Sometimes you have to work with base::plot and to combine multiple plots the solution is e.g. par(mfrow=c(1,2), ...). Unfortunately using par can mess up all your future plots in the active R session. This is one handy trick to get back to the default settings for plotting:

op = par(mfrow = c(1, 2))
plot(runif(100), runif(100))
plot(runif(100), runif(100))

plot of chunk unnamed-chunk-1

par(op)
plot(runif(100), runif(100))

plot of chunk unnamed-chunk-1