Growing a tree using R and ggtree part 2

Adding tip labels

In addition to adding a heatmap I found that adding coloured shapes to tips was a useful feature

• First off read and plot the tree as before

  tree <- read.tree("/path/to/newick/tree")
  p <- ggtree(tree, right = TRUE)
  plot(p)
  

• Next read in an additional tsv file with taxa names in the first column and meta data to plots as shapes in additional columns

# read in tiplabel metadata
tip_metadata <- read.table("meta_data.txt", sep="\t", header=TRUE,check.names=FALSE, stringsAsFactor=F)

The format for this is as follows:

• This data can then be plotted as tip labels where the colours are either determined randomly

p <- p %<+% tip_metadata + geom_tippoint(aes(color=age_group), size=3)
plot(p)

• Or if you want to enter them manually use the scale_color_manual functionality where colours are assigned to the column values based on alphabetical order

p <- p %<+% tip_metadata + geom_tippoint(aes(color=age_group), size=3) + scale_color_manual(values=c("red", "blue","green","grey"))
plot(p)

• The shapes can be altered based on another columns

p <- p %<+% tip_metadata + geom_tippoint(aes(color=age_group, shape=country_of_residence), size=3) + scale_color_manual(values=c("red", "blue","green","grey"))

• To specify the shapes manually use the + scale_shape_manual function

p <- p %<+% tip_metadata + geom_tippoint(aes(color=age_group, shape=country_of_residence), size=3) + scale_color_manual(values=c("red", "blue","green","grey")) + scale_shape_manual(values=c(1,2,3))

The shape numbers can be found here