Plotting device with RStudio

Question

I have issue with plotting lines over my existing plot in .Rmd in RStudio. I ran the code within the code chunk in .Rmd (⌘ + return) and the plot gives me a graph within the .Rmd (new feature of RStudio v1.0), however when I ran the second code lines , an error shows up.

plot(density(with$glucose), 
     ylim = c(0.00, 0.02),
     xlab = "Glucose Level",
     main = "Figure",
     lwd = 2)
lines(density(without$glucose), 
      col = "red",
      lwd = 2)
Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet

On the other hand, if I copy and paste the codes into the console, I could get the plot I want, in the plot viewer within RStudio.

In addition, when I ran some other codes within the .Rmd (⌘ + return), my plots in the plot viewer in RStudio disappear. This means I have to do copy-paste into the console instead of using the (⌘ + return) shortcut.

Does anyone have the same problem?

Answer 1

This is a known problem, but you can solve it very easy: Press Ctrl+Shift+Enter to run the complete chunk, then everything works fine and you don't have to copy-and-paste all thing to the console. So do all your plots in one chunk and run this chunk. This will produce you the plot within the RMD file (as you mentioned: new feature of RStudio 1.0)

Answer 2

If you're not a fan of the inline output / notebook mode for R Markdown documents, you can also disable it within the Global Options dialog -- try disabling the option:

• Show output inline for all R Markdown document