Plot symbols not showing properly using R + knitr with 'pdf' device

Question

When I include R plots in a latex document using knitr, symbols do not show properly when knitr's graphic device is 'pdf', while everything is OK when the graphic device is 'png'. Here is a MWE:

\documentclass{article}

<<>>=
library(knitr)
library(survival)
attach(lung)
@ 

\begin{document}

A sample figure with default 'pdf' device.

<<>>=
plot(age, meal.cal)
@ 
\clearpage

Same figure, with 'png' device.

<<dev='png'>>=
plot(age, meal.cal)
detach(lung)
@ 
\end{document}

Here is the result: https://drive.google.com/open?id=1fz_6XuDxdDWNhX_EWRnUYInSG-pklkuA

In the first graph the circles are not drawn, while the second graph is fine. Any suggestion?

Answer 1

The default pdf device in R uses a character from the ZapfDingbats font for the circles in the graph. However, the font is not embedded in the pdf file, therefore a pdf viewer does not display the circles when the font or a suitable replacement is not found (to the defense of R: ZapfDingbats is one of the Standard 14 Fonts, i.e., several variants of Times, Helvetica, Courier, Symbol and ZapfDingbats). See the font properties of the pdf file created using the pdf device:

The cairo_pdf device can be used instead. This device does not use a circle character from a font (the circle is drawn directly). Moreover, all fonts are embedded.

Relevant code:

\begin{document}

A sample figure with default 'pdf' device.

<<dev='cairo_pdf'>>=
plot(age, meal.cal)
@ 
\end{document}

Example font properties:

Note that with cairo_pdf the circles are not selectable/searchable, but that is not likely to be a problem.