Problem Summary: ggplot2 graphs seem to be of poor quality in shiny, when hosted on shinyapps.io. Graph elements contain visible defects, e.g. dots of
Since you're probably on a Linux-based server, you will likely need to use the Cairo graphical library.
Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB. Cairo is designed to produce consistent output on all output media while taking advantage of display hardware acceleration when available (eg. through the X Render Extension). Personally, I use it for the alpha channel (transparency options).
Conveniently, there is an R implementation that creates a cairo graphics device in the "Cairo" package. In effect, you have to add the following chunk to 'server.R':
#install.packages("Cairo")
library(Cairo)
options(shiny.usecairo=T)
That should do it.
PS: I see @MathewPlourde already answered this question in the comments.