Awesome

ggtree version of plotTree

plotTree (Plotting trees with data using R and Python) is developed by Kat Holt - @DrKatHolt - http://holtlab.net.

This repository used example data of the plotTree to re-create figures using ggtree.

ggtree is far better than plotTree, please refer to our manuscript published on Molecular Biology and Evolution and the supplemental files for more detail information.

Basic strain info

source("01_basic_strain_info.R")

Pan genome heatmap

source("02_pan_genome_heatmap.R")

Curated genes, coloured

source("03_curated_genes.R")

Plot tree with data

# in case colnames start with numbers or contain dashes, which R does not like as column headers
snps<-read.csv("plotTree/tree_example_april2015/alleles.csv",header=F,row.names=1, stringsAsFactor=F) 
snps_strainCols <- snps[1,] # column names = strain names
snps<-snps[-1,] # drop strain names
colnames(snps) <- snps_strainCols

gapChar <- "?"
snp <- t(snps)
lsnp <- apply(snp, 1, function(x) x != snp[1,] & x != gapChar & snp[1,] != gapChar)
lsnp <- as.data.frame(lsnp)
lsnp$pos <- as.numeric(rownames(lsnp))
lsnp <- tidyr::gather(lsnp, name, value, -pos)

## dataset 1
snp_data <- lsnp[lsnp$value, c("name", "pos")]
head(snp_data)

##              name     pos
## 394 10014_HCMC_NA 2090164
## 401 10014_HCMC_NA 1357659
## 409 10014_HCMC_NA 3145957
## 419 10014_HCMC_NA 4902236
## 484 10014_HCMC_NA 1339574
## 498 10014_HCMC_NA  354844

## dataset 2
bar_data <- read.csv("plotTree/tree_example_april2015/bar.csv")
head(bar_data)

##                  id dummy_bar_value
## 1  CS14_Brazil_2001               5
## 2   CS2_Brazil_1997              10
## 3  CS20_Brazil_2002               2
## 4   CS6_Brazil_2000               7
## 5   CS7_Brazil_2000               8
## 6 373_Cameroun_1973              10

library(ggtree)

info <- read.csv("info.csv")
tree <- read.tree("tree.nwk")

p <- ggtree(tree) %<+% info + geom_tippoint(aes(color=location))

facet_plot(p, panel="SNP", data=snp_data, geom=geom_point, mapping=aes(x=pos), pch='|', color="firebrick") %>%
    facet_plot("BAR", bar_data, geom_segment, aes(x=0, xend=dummy_bar_value, y=y, yend=y)) + theme_tree2()