How can I save multiple sequential plots generated by one function in R?

Question

Some functions can draw a plot for each of multiple data. So it looks like a movie with many plots shown one after another very quickly. Examples of such functions including plot and gelman.plot of the output returned by BRugsFit(), when there are many parameters and each plot for each parameter.

Because it flashes too fast, I want to examine each plot carefully before looking at the next plot. So I would like to save the plots into files, (if not possible, I would hope to slow down the flashing or at least have some control).

1. To save the plots, I try to put them into a single figure, but I haven't figured out how to do that successfully (note that I run R in bash terminal, not using any IDE such as RStudio):

   > pdf('gelman.pdf')
   > par(mfrow=c(10,10)); gelman.plot(output,auto.layout=F,autoburnin=F)
   Error in plot.new() : figure margins too large
   > dev.off()
   null device 
             1 
   > 
   > pdf('tracedensity.pdf')
   > par(mfrow=c(10,14)); plot(output,auto.layout=F)
   Error in plot.new() : figure margins too large
   > dev.off()
   null device 
             1
   

2. Alternatively, I wonder if I can save each plot into a different pdf file? Or group a smaller number of plots into several files?

Thanks!

Answer 1

Get rid of the par - which means you're trying to fit all the graphs on one page, but the error about figure margins means R isn't able to fit them on the same page so is producing no output. The remaining code will produce a multi-page pdf, one chart per page.

Alternatively, if you must have them on the same page, then use a larger page pdf('gelman.pdf', height=70, width=70) should do it.