03_curated_genes.R

library(ggtree)

oldwd <- getwd()
setwd("plotTree/tree_example_april2015/")

info <- read.csv("info.csv")
tree <- read.tree("tree.nwk")
cols <- c(HCMC='black', Hue='purple2', KH='skyblue2')

heatmap.colours=c("white","grey","seagreen3","darkgreen","green","brown","tan","red","orange","pink","magenta","purple","blue","skyblue3","blue","skyblue2")
names(heatmap.colours) <- 0:15

heatmapData=read.csv("res_genes.csv", row.names=1)
rn <- rownames(heatmapData)
heatmapData <- as.data.frame(sapply(heatmapData, as.character))
rownames(heatmapData) <- rn


p <- ggtree(tree) %<+% info +
    geom_tippoint(aes(color=location)) + scale_color_manual(values=cols) +
    geom_tiplab(aes(label=name), align=T, linetype=NA, size=2, offset=4, hjust=0.5) +
    geom_tiplab(aes(label=year), align=T, linetype=NA, size=2, offset=8, hjust=0.5)
    
p2 <- gheatmap(p, heatmapData, offset = 10, color=NULL, colnames_position="top", colnames_angle=90, colnames_offset_y = 1, hjust=0, font.size=2) +
    scale_fill_manual(values=heatmap.colours, breaks=0:15)


setwd(oldwd)
print(p2)