tanglegram.Rmd

---
title: "tanglegram"
author: "Le Viet Thanh"
date: "July 24, 2017"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
#Library from CRAN
library(ape) #nj tree
library(dendextend) #tanglegram
library(dplyr) #pipe
library(randomcoloR) #random distinct colors
#Library from Bioconductor
library(DECIPHER) #load dendrogram tree
```


## 1. Generating some trees
```{r}
den <- read.nexus.data("dengue.nex") %>% as.DNAbin()

#Estimate distance
den.dist <- dist.dna(den, as.matrix = TRUE) 

#bionj
den.tree.bionj <- bionj(den.dist)
#Remove neg branch length
den.tree.bionj$edge.length[den.tree.bionj$edge.length < 0] <- 0 
den.tree.bionj <- chronos(den.tree.bionj)
write.tree(den.tree.bionj, "den_bionj.nwk")


#nj
den.tree.nj <- nj(den.dist)
#Remove neg branch length
den.tree.nj$edge.length[den.tree.nj$edge.length < 0] <- 0 
den.tree.nj <- chronos(den.tree.nj)
write.tree(den.tree.nj, "den_nj.nwk")
```

## 2. Tanglegram

### Preparing data

```{r}
den_nj <- ReadDendrogram("den_nj.nwk") %>% as.dendrogram()
den_bionj <- ReadDendrogram("den_bionj.nwk") %>% as.dendrogram()

labels <- den_nj %>% set("labels_to_char") %>% labels
labels <- as.data.frame(labels)
labels$country <- gsub("D4|[0-9]{2}","",labels$labels)

unique_country <- data.frame(country = unique(labels$country))

unique_country$color <- distinctColorPalette(nrow(unique_country))

labels_color <- left_join(labels, unique_country)
den_list <- dendlist(den_bionj, den_nj)

```

### Fig 1

- hang = FALSE

```{r}
tanglegram(den_nj, den_bionj, 
           highlight_branches_lwd = FALSE,
           common_subtrees_color_lines = FALSE,
           highlight_distinct_edges = FALSE,
           hang = F,
           lwd = 1.5,
           edge.lwd = 2,
           color_lines = labels_color$color,
           sort = FALSE,
           columns_width = c(4,4,4),
           intersecting = FALSE,
           margin_outer = 1.6,
           margin_inner = 6,
           dLeaf = 0.00000000005,
           main = "Colored by Country",
           cex_main = 1)
```


### Fig 2

- hang = TRUE

```{r}
tanglegram(den_nj, den_bionj, 
           highlight_branches_lwd = FALSE,
           common_subtrees_color_lines = FALSE,
           highlight_distinct_edges = FALSE,
           hang = T,
           lwd = 1.5,
           edge.lwd = 2,
           color_lines = labels_color$color,
           sort = FALSE,
           columns_width = c(4,4,4),
           intersecting = FALSE,
           margin_outer = 1.6,
           margin_inner = 6,
           dLeaf = 0.00000000005,
           main = "Colored by Country",
           cex_main = 1)
```