joey711/phyloseq — pull request #160 by gjuggler (2013-01-14 22:42:20+00:00)
Title: Add some new features to the tree plots

(See some screenshots attached below. The Gist used to create the plots is here: https://gist.github.com/4534173)

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.

![01_ladderize_left](https://f.cloud.github.com/assets/51842/66194/7c40f448-5e9b-11e2-95f4-a15a2e1dee2b.png)
![02_ladderize_right](https://f.cloud.github.com/assets/51842/66195/7ee8b6fe-5e9b-11e2-886e-5c9341ee3f73.png)
![03_lots_of_space](https://f.cloud.github.com/assets/51842/66196/82ea891c-5e9b-11e2-82a5-18d74e76806f.png)
![04_brewer_colors](https://f.cloud.github.com/assets/51842/66197/87e44944-5e9b-11e2-95fe-2dc7f6cea925.png)
![05_manual_colors](https://f.cloud.github.com/assets/51842/66199/8a4d5ab8-5e9b-11e2-945e-6cb521aa7f3d.png)