Tree plots: ladderize, margins, color scales

This commit adds a few features to the tree plots that were requested
by a user:

1) Ladderization. This commit fixes a bug in the tree layout code, so
now the ladderize() function from ape now correctly affects the tree
layout. A ladderize parameter was added to the main plot function.

2) Margins. A plot.margin parameter was added to the plot function, to
let users add extra space to the right of the tree when long taxa
names are being truncated.

3) Color scales. A color.scale parameter was added to let users
specify their own ggplot color scale for the sample points.
Merge pull request #160 from gjuggler/master

Add some new features to the tree plots, better formatting and additional options.

Will roll back after committing pull to drop it into "fixes" branch for some tidying. Looks pretty good so far...