Reposition the labels on ggtree

Question

I am trying to visualize my ggtree and I seem to be stuck on the last final step; repositioning the tree labels from horizontal to verticle so that they do not overlap. If I change the geom = "text" on the geom_tiplab function, I get what I want but my labels are no longer coloured. Datasets here and here

Here is the code for reproducibility; Please help

p1 <- ape::read.tree("Tert_aln.fasta_processed.fa.raxml.support")
temp1 = read.csv("Tert_Final_Mapping_File.csv", sep=";")
mycolors = c(brewer.pal(name="Set1", n = 9), brewer.pal(name="Paired", n = 12), brewer.pal(name="Dark2", n = 8))
p2 <- ggtree(p1, layout='circular') %<+% temp1 +
  geom_tippoint(
    mapping = aes(color = phylum),          # tip color by phyla. 
    size = 2,
    show.legend = FALSE) +
  scale_color_manual(values = mycolors) +
  geom_tiplab(                          # adds name of phyla to tip of its branch
    aes(fill = phylum),
    color = 'black',                      
    offset = 2,
    size = 3,
    geom = "label",
    align = TRUE,
    face = "bold",
    label.size = 0
    label.padding = unit(0.15, "lines"), # amount of padding around the labels
    linetype = "solid") +
  ggtitle("Phylogenetic tree of Tert")+  # title of your graph
  theme(
    axis.title.x = element_blank(), # removes x-axis title
    axis.title.y = element_blank(), # removes y-axis title
    legend.title = element_text(    # defines font size and format of the legend title
      face = "bold",
      size = 12),   
    legend.text=element_text(       # defines font size and format of the legend text
      face = "bold",
      size = 10),  
    plot.title = element_text(      # defines font size and format of the plot title
      size = 12,
      face = "bold"),  
    legend.position = "bottom",     # defines placement of the legend
    legend.box = "vertical",        # defines placement of the legend
    legend.margin = margin()) 
pdf("ggplot_Tert1.pdf", width = 20, height = 22)
p2
dev.off()

Answer 1

I noticed you wrote you wanted colored labels, but you have fill, which isn't doing anything here. You declared color = 'black', as well.

Sorry if I miss the mark! I am applying my best guess as to what you wanted to see.

There are four things I did to make this happen:

• 1. In geom_tiplab(), I changed fill = phylum to color = phylum.
• 2. In geom_tiplab(), I commented out color = 'black'.
• 3. In geom_tiplab(), I commented out label.size = 0.
• 4. In geom_tiplab(), I changed geom = "label" to geom = "text".

Is this what you wanted? (You will have to adjust the plotted limits to get all of the text into the visual.) This is geom = "text". When you use labels, it automatically rotates the values to show horizontally.