(This article was first published on theBioBucket*, and kindly contributed to R-bloggers)
...Just read you JPEG and add an alpha channel manually, then assign values for transparency. Of course for printing you need to use a device that accepts alpha.
See how it's done HERE.
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).