Merge pull request #157 from joey711/fixes

v1.3.3 updates to import_qiime, modular tax_table build
Merge pull request #158 from joey711/fixes

v1.3.4 merge_samples doc update, v-reqs, tests
Merge pull request #159 from joey711/fixes

v1.3.5 Updated README
v1.3.6 Updated basics vignette
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...
Revert "Merge pull request #160 from gjuggler/master"

This reverts commit 9bbcf07f09225751fe5f8533d5ddf5645b6db377, reversing
changes made to 3270a0bf462325ca8fa1dd3e1f2700f000d4df7f.
Revert "Revert "Merge pull request #160 from gjuggler/master""

This reverts commit c5383776cfd4a434b4313ee712f9005810e699e4.
v1.3.7 conflict resolution during re-merge
Fixed issue with ordering in doc
merge-related fixes and update to plot_tree examples
unfortunate conflict issues already fixed in master