Add geom_hilight for phyla.

[MjelleLab]

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I would like to add a geom_hilight for each phyla from the tip all the way to the root of each phylum. Here is my script and the table below with IDs of the tips and Phyla. Any tips appreciated.

p <- ggtree(tree.HMF.ape,ladderize = T, layout="fan", open.angle=12, size=0.2,right = T) 

p1 <- p +
  geom_fruit(
    data=split.treeoflife,
    geom=geom_point,
    mapping=aes(y=SGB, colour=Phylum,fill=Phylum),
    position="identity",
    size=3
  ) +

  
scale_size_continuous(
    range=c(1, 3), # the range of size.
    guide=guide_legend(
      keywidth=0.5, 
      keyheight=0.5,
      order=2
    )
  ) +
  scale_fill_manual(
    values=c("#8c510a","#276419","#b2182b","#2166ac","#fee090","#B0BEC5")
  ) +
scale_colour_manual(
  values=c("#8c510a","#276419","#b2182b","#2166ac","#fee090","#B0BEC5"))
p1
p1 + 
new_scale_fill() +
  geom_fruit(
    data=p.dat2,
    geom=geom_tile,
    mapping=aes(y=SGB,x=ring_alpha, alpha=MeanPrevalence, fill=ring_alpha),
    pwidth=0.05,

      axis.params=list(
      axis="x", # add axis text of the layer.
      text.angle=-45, # the text angle of x-axis.
      hjust=0,  # adjust the horizontal position of text of axis.
    )
  ) +
  
scale_fill_manual(
    values=c("#081d58", "#67000d"),
    guide=guide_legend(keywidth=0.5, keyheight=0.1, order=4,title = "Sample type")
  ) +
  scale_alpha_continuous(
    range=c(0, 1), # the range of alpha
    guide=guide_legend(keywidth=0.5, keyheight=0.3, order=5,title = "Abundance")
  ) 

> head(split.treeoflife)
          Phylum         Class           Order           Family        Genus                  Species            SGB
1 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae  Actinomyces     Actinomyces_SGB17154       SGB17154
2 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae  Actinomyces Actinomyces_graevenitzii       SGB17130
3 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae  Actinomyces     Actinomyces_sp_ICM47       SGB17167
4 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae Actinotignum   Actinotignum_timonense SGB17174_group
5 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae  Fannyhessea      Fannyhessea_vaginae         SGB991
6 Actinobacteria Actinomycetes Actinomycetales Actinomycetaceae      Gleimia         Gleimia_europaea       SGB17196