Add tree_subset method for both phylo and treedata objects

[tbradley1013]

Description

This PR adds a function for subsetting phylogenetic trees by specifying the desired node to focus on and the number of ancestry levels back to look. It returns an object of class phylo or treedata, depending on the input, with all related nodes to the one specified.

Related Issue

This fixes YuLab-SMU/tidytree#5 and is related to a similar PR (YuLab-SMU/tidytree#6) but moved the implementation to this package rather then tidytree.

Example

library(treeio)
library(ggplot2)
library(ggtree)
#> ggtree v1.13.0.002  For help: https://guangchuangyu.github.io/software/ggtree
#> 
#> If you use ggtree in published research, please cite:
#> Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628

set.seed(42)

# example with a phylo object
bi_tree <- ape::rtree(10)
bi_tree$tip.label <- paste0("t", 1:10)

bi_tree %>% 
  ggtree() +
  geom_tiplab()

bi_subset <- tree_subset(bi_tree, "t5", 4)

bi_subset %>% 
  ggtree(aes(color = group)) + 
  geom_tiplab() +
  scale_color_manual(values = c(`1` = "red", `0` = "black"))

#example with treedata object
beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")
rst_file <- system.file("examples/rst", package="ggtree")
mlc_file <- system.file("examples/mlc", package="ggtree")
beast_tree <- read.beast(beast_file)
codeml_tree <- read.codeml(rst_file, mlc_file)

merged_tree <- merge_tree(beast_tree, codeml_tree)

merged_tree %>% 
  ggtree() + 
  geom_tiplab() +
  theme_tree2() +
  lims(x = c(0, 25))

merged_subset <- tree_subset(merged_tree, "A/Swine/GX/2242/2011", 3)

merged_subset %>%
  ggtree(aes(color = group)) + 
  geom_tiplab() +
  scale_color_manual(values = c(`1` = "red", `0` = "black")) +
  theme_tree2() +
  lims(x = c(0, 2))

Created on 2018-05-23 by the reprex package (v0.2.0).

Tests

All tests can be found in tests/testthat/test-tree-subset.R and all tests pass when devtools::test() is run

[GuangchuangYu]

thanks @tbradley1013 , pls add your name in author list as a contributor. I do want to acknowledge all contributors.