Fixed some bugs in Chapter 3 R code:

* Use 'ggsave' instead of 'pdf' (was not actually saving PDF files before)
* replaced deprecated 'opts' with 'theme'
* use 'stat="identity" in the geom_bar calls
* use 'colMeans' instead of 'mean' for data frame
Merge pull request #3 from anyonecancode/ch3-bugfixes

Fixed some bugs in Chapter 3 R code: