treespace_mrbayes.Rmd

---
title: "Treespace plots (mrbayes)"
author: "Michelle Kendall and John Lees"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---
  
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, dpi=96, fig.width=9, fig.height=8, dev="png")
```

First, load packages and data:
  
```{r load_packages, message=F}
library(treespace)
library(ggplot2)
library(here)
# NB this assumes the trees are in the project directory, or specfically wherever "here()" points
mrbayes_tr <- readRDS(here("mrbayes_trees.rds"))
```

### Clustering

Treespace analysis:
```{r initial_treespace}
mrbayes_treespace = treespace(mrbayes_tr, nf=3)
```

Colouring the trees by type:
  
```{r treeTypes}
treeTypes = c("True", rep("Chain1", 66), rep("Chain2", 66))
plotGrovesD3(mrbayes_treespace$pco, treeNames=names(mrbayes_tr), groups=treeTypes,
             colors=c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442"),
             labels_size=6)
```