Fig4_RAXMLtree.Rmd

---
title: "Fig 3. RAXML tree"
author: "Shankar K Shakya"
date: "February 26, 2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}

rm(list =ls())
library(ape)
#mytree <- read.tree("RAxML_bestTree.Ind205_results")
mytree <- read.tree("205Isolates_RAXML/RAxML_bipartitions.Ind205_results")

#mytree <- read.tree("ASC_MULTIGAMMA/RAxML_bipartitions.Ind205_results_MULTIGAMMAI")
mytree$tip.label

mytree <- drop.tip(mytree, "Psojae")

id <- unlist(strsplit(mytree$tip.label, split = ".fq"))
pcinna_pop <- read.csv("New Microsoft Excel Worksheet.csv", header = TRUE)
pcinna_pop <- pcinna_pop[pcinna_pop$Isolate %in% id, ]
pcinna_pop <- pcinna_pop[match(id, pcinna_pop$Isolate), ]
pop_cinna_continent <- pcinna_pop$Continent

continent <- as.character(pcinna_pop$Continent)
country <- as.character(pcinna_pop$Country)

continent[grep("Taiwan", country)] <- "Taiwan"
continent[grep("Vietnam", country)] <- "Vietnam"

country_continent_mixpop <- continent
new_pop <- country_continent_mixpop

tips <- unlist(strsplit(mytree$tip.label, split = ".fq"))
tips <- unlist(lapply(strsplit(tips, "-"), function(x) x[2]))

len <- length(which(duplicated(tips)))
tips[which(duplicated(tips))] <- paste0(seq(1:len), tips[which(duplicated(tips))])

mytree$tip.label <- tips

ids <- as.data.frame(mytree$tip.label)

ids[2] <- new_pop
rownames(ids) <- ids$`mytree$tip.label`
ids <- ids[2]
ids <- as.matrix(ids)[, 1]

tree <- mytree
x <- ids


library(pals)
library(phytools, quietly = T, verbose = F)
library(RColorBrewer)

#tiff("./FIGS/RAXML_tree.tiff", width = 10, height = 7, units = "in", res = 600)

# plot(ladderize(tree, right = F), type = "fan", show.tip.label = FALSE)
# mycol <- c("#0000FF", "#FFFF00","#ff0000","#00FFFF","#000000","#FFC0CB","#00ff00", "#FF00FF") %>% setNames(unique(new_pop))
# cols <- setNames(mycol[1:length(unique(x))],sort(unique(x)))
# tiplabels(pie=to.matrix(x,sort(unique(x))), piecol = mycol,cex=0.25)
# add.simmap.legend(colors=cols,x=0.9*par()$usr[1], y=0.9*par()$usr[4],prompt=FALSE,fsize=0.9)
# add.scale.bar()

#dev.off()

######### Bootstrap support

#tiff("./FIGS/FanBootstrap_RAXML_tree.tiff", width = 12, height = 12, units = "in", res = 600)

mycol <- c("#0000FF", "#FFFF00","#ff0000","#00FFFF","#000000","#FFC0CB","#00ff00", "#FF00FF") %>% setNames(unique(new_pop))

plot.phylo(ladderize(tree, right = F), show.tip.label = FALSE, use.edge.length = T, type = "fan")

cols <- setNames(mycol[1:length(unique(x))],sort(unique(x)))
tiplabels(pie=to.matrix(x,sort(unique(x))), piecol = mycol,cex=0.2)
add.simmap.legend(colors=cols,x=0.9*par()$usr[1], y=0.9*par()$usr[4],prompt=FALSE,fsize=0.9)
mynode <- tree$node.label
mynode[mynode < 85] <- NA
nodelabels(mynode, adj = c(1,1.5), frame = "n", cex = 0.7, pch = 12, horiz = T)
add.scale.bar(x = -1, y = -1)

#dev.off()























population <- pcinna_pop$Continent
countryInfo <- split(tree$tip.label, population)
tree2 <- groupOTU(tree, countryInfo)
tree2$tip.label <- paste(population, pcinna_pop$MT, sep = "_")

ggtree(tree2) + geom_tiplab(size=3, align = T)


ggtree(tree2, aes(color=group, label = node), layout="circular", ladderize = TRUE) + geom_tiplab(size=3, aes(angle=angle))





```