Tblog.R

#code based on functions from: https://thackl.github.io/ggtree-composite-plots

library(ggtree)
library(patchwork)

no_legend <- function() theme(legend.position="none")

tree_y <-  function(ggtree, data){
  if(!inherits(ggtree, "ggtree"))
    stop("not a ggtree object")
  left_join(select(data, label), select(ggtree$data, label, y)) %>%
    pull(y)
}

# overwrite the default expand for continuous scales
scale_y_tree <- function(expand=expand_scale(0, 0.6), ...){
  scale_y_continuous(expand=expand, ...)
}

# get the range of the ggtree y-axis data
tree_ylim <- function(ggtree){
  if(!inherits(ggtree, "ggtree"))
    stop("not a ggtree object")
  range(ggtree$data$y)
}

# plot data next to a ggtree aligned by shared labels
ggtreeplot <- function(ggtree, data = NULL, mapping = aes(), flip=FALSE,
                       expand_limits=expand_scale(0,.6), ...){
  
  if(!inherits(ggtree, "ggtree"))
    stop("not a ggtree object")
  
  # match the tree limits
  limits <- tree_ylim(ggtree)+c(-5,0)#JZ added
  limits[1] <- limits[1] + (limits[1] * expand_limits[1]) - expand_limits[2]
  limits[2] <- limits[2] + (limits[2] * expand_limits[3]) + expand_limits[4]
  
  if(flip){
    mapping <- modifyList(aes_(x=~x), mapping)
    data <- mutate(data, x=tree_y(ggtree, data))
    gg <- ggplot(data=data, mapping = mapping, ...) +
      scale_x_continuous(limits=limits, expand=c(0,0))
  }else{
    mapping <- modifyList(aes_(y=~y), mapping)
    data <- mutate(data, y=tree_y(ggtree, data))
    gg <- ggplot(data=data, mapping = mapping, ...) +
      scale_y_continuous(limits=limits, expand=c(0,0))
  }
  gg
}

# get rid of superfluous axis - this works after coord_flip, so it also works
# for the rotated histogram
no_y_axis <- function () 
  theme(axis.line.y = element_blank(), 
        axis.title.y = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank())