overlaping-clades (1).R

In jennahamlin/annoatater: An Amazing Shiny App

# BiocManager::install("treeio")
# BiocManager::install("ggtree")

library(treeio)
library(ggtree)
library(ggplot2) # to pre-build the plot
library(DescTools) # easy checking if ranges overlap

#
tree <- treeio::read.newick("C:/Users/ptx4/Desktop/example.data.for.testing/1504MLEXH-1/1504MLEXH-1.dnd")

tree_plot <-
  ggtree::ggtree(tree) +
  ggtree::geom_tiplab() +
  ggplot2::xlim(NA, 0.02)

 tip_vectorAll<-c()
# 
# print(tip_vector)
# 
#  tip_vector <-
#   list(
#     c("2015C-3893_fastx5", "PNUSAE000514_fastx5"),
#     c(
#       "2015C-3893_fastx5",
#       "PNUSAE000514_fastx5",
#       "PNUSAE000632_fastx5"
#     )
#   )
# print(tip_vector)

tip_vector <-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5"))
tip_vector2 <-list(c("2015C-3893_fastx5", "PNUSAE000514_fastx5", "PNUSAE000632_fastx5"))


make_layer <- function(tree, tips, label, color, offset) {
  ggtree::geom_cladelabel(
    node = phytools::findMRCA(ape::as.phylo(tree), tips),
    label = label,
    color = color,
    angle = 0,
    offset = offset
  )
}

check_overlap <- function(previous_plot, incoming_tips) {
  pre_g <- ggplot2::ggplot_build(previous_plot)
  
  tip_labels <- pre_g$data[[3]]
  
  incoming_y_coords <-
    tip_labels[tip_labels$label %in% incoming_tips, "y"]
  
  # print(incoming_y_coords <-
  #       tip_labels[tip_labels$label %in% incoming_tips, "y"]
  # )
  
  if (length(pre_g$data) < 4) {
    any_overlap <- FALSE
  } else {
    
    clade_segments <- pre_g$data[[4]]
    #print(clade_segments <- pre_g$data[[4]])
    
    overlaps <- sapply(1:nrow(clade_segments), function(i) {
      X <- DescTools::Overlap(
        x = c(clade_segments[i, "y"], clade_segments[i, "yend"]), 
        y = incoming_y_coords)
      Y <- X > 0
      #return(Y)
    })
    #print(overlaps)
    #any_overlap <- any(overlaps)
  }
  #return(any_overlap)
}



#tip_vectorAll <- c(tip_vectorAll, tip_vector2)

add_annotations <- function(tree_plot, tip_vector) {
  g <- tree_plot
  #print(g$data)
  
  for (i in seq_along(tip_vector)) {
    
    #print(tip_vectorAll)
    #print(tip_vector)
    #tip_vector[i] <- tip_vector[i]
    
    any_overlap <- check_overlap(previous_plot = g, incoming_tips = tip_vector[[i]])
    print(tip_vector[[i]])
    # current_offset <- ifelse(any_overlap, 0.011, 0.008)
    
    print(any_overlap)                                                                           
    #print(current_offset)
    
    g <- g +
      make_layer(
        tree_plot,
        tips = tip_vector[[i]],
        label = paste("Clade", i),
        color = rev(colors())[i],
        offset = current_offset <- ifelse(any_overlap, 0.011, 0.008)
      )
  }
  return(g)
}

for (i in 1:length(tip_vector))
  tip_vectorAll <- c(tip_vectorAll, tip_vector)

print(tip_vectorAll)

add_annotations(tree_plot = tree_plot, tip_vector = tip_vectorAll)