Some objects (functions) of ggplot2 support an alpha channel. http://docs.ggplot2.org/current/geom_point.html This is a nice feature, but transparent colours in pdf and png files are often source of diversified trouble. How can I use the alpha option and get flattened pdf output files? I had ongoing problems with a large Latex doc created with knitr + ggplot that was perfectly readable on my mac but was unopenable for Windows users. After numerous attempts at optimizing and flattening the pdf, I finally isolated the issue to a single alpha-heavy plot. In my case, switching from pdf to png