Made some minor edits to your code, mostly to fix new ggplot2 and add in some libraries. Was thwarted by the twitter chapter because invariably there were some Inf values that hclust did not like.
removed deprecated ggplot2 parameters
now ignoring pdfs
removed legend argument in scale_alpha
updated to new ggplot2 params
minor edits to new ggplot2
Added HMisc package to installer list
added Hmisc to package_installer
format package installer
edited y-axis labels
updated to new ggplot2 parameters, added reshape
updated to handle error messages
This looks amazing, Zach. We actually just made some changes that conflict with this, so we'll have to cherry-pick changes or do some reverting to make this work. We'll get to that after Strange Loop in a week.
Any chance you've got a moment to see what happens if you run a git pull origin master? I've incorporated a lot of your changes, so it would be great to try to narrow down on those that are still needed.
git pull origin master
updated to JMW changes
fixed bad merge, updated to JMW edits