practice.md

Practice

Load libraries

library(ape)
library(ggplot2)
library(ggtree)
library(phylobase)

Read in tree

read.tree is used to read in a Newick formatted tree.

tr <- read.tree("mers_subtree.tre")
tr

## 
## Phylogenetic tree with 9 tips and 8 internal nodes.
## 
## Tip labels:
## 	KM027258_Human_2014/04/12, KM027255_Human_2014, KM027261_Human_2014/04/15, KM027259_Human_2014/04/14, KM027256_Human_2014, KM027260_Human_2014/04/21, ...
## Node labels:
## 	1.0, 1.0, 0.9876111111111111, 0.1333888888888889, 0.9997222222222222, 0.1065, ...
## 
## Rooted; includes branch lengths.

Let's look closer at the tree object.

names(tr)

## [1] "edge"        "Nnode"       "tip.label"   "edge.length" "node.label"

tr$edge

##       [,1] [,2]
##  [1,]   10   11
##  [2,]   11   12
##  [3,]   12    1
##  [4,]   12   13
##  [5,]   13   14
##  [6,]   14    2
##  [7,]   14    3
##  [8,]   13   15
##  [9,]   15   16
## [10,]   16    4
## [11,]   16    5
## [12,]   15    6
## [13,]   11    7
## [14,]   10   17
## [15,]   17    8
## [16,]   17    9

tr$Nnode

## [1] 8

tr$tip.label

## [1] "KM027258_Human_2014/04/12" "KM027255_Human_2014"      
## [3] "KM027261_Human_2014/04/15" "KM027259_Human_2014/04/14"
## [5] "KM027256_Human_2014"       "KM027260_Human_2014/04/21"
## [7] "KM027257_Human_2014/04/07" "KJ713296_Camel_2013/11"   
## [9] "KJ713295_Camel_2013/11"

tr$edge.length

##  [1] 0.67659 0.12212 0.19232 0.04783 0.10851 0.02722 0.04420 0.03124
##  [9] 0.02702 0.09171 0.00408 0.13791 0.30074 0.28475 0.30305 0.30470

tr$node.label

## [1] "1.0"                 "1.0"                 "0.9876111111111111" 
## [4] "0.1333888888888889"  "0.9997222222222222"  "0.1065"             
## [7] "0.15838888888888888" "1.0"

Extract annotations

host <- tr$tip.label %>% strsplit(.,"_") %>% lapply(.,"[",2) %>% unlist
dd <- data.frame(taxa=tr$tip.label,host=host)

Plot using ape

The plotting function in ape only requires a single argument, the tree.

plot(tr)

plot(tr)
add.scale.bar()

Generate ggtree and add annotations

g <- ggtree(tr,right=TRUE,time_scale=TRUE) %<+% dd

Plot tree

g+
  theme_tree2()+ # time scale
  geom_point(subset=.(isTip),aes(shape=host,color=host),size=4)+ # tip symbols
  geom_text(aes(color=host,label=host),hjust=-0.1)+ # tip labels
  xlim(0,1.2)+ # x scale
  xlab("Time") # x label

## Error in eval(expr, envir, enclos): could not find function "geom_point"