R/plot_refs.R

In LBMC/zebraRef: Zebrafish Reference Data For The RAPToR Package

#' Plot Reference Timelines
#' 
#' Plots the coverage of the `zebraRef` references (requires ggplot2)
#' 
#' @examples 
#' \donttest{
#' .plot_refs()
#' }
#' 
#' @export
#' 
#' @importFrom rlang .data
.plot_refs <- function(){
  if(!requireNamespace("ggplot2")){
    message("Install ggplot2 to see this graph !")
  }
  dat <- zebraRef::Dre_devstages
  
  lbs <- data.frame(tunit = unique(dat$devstages$tunit), lab = c("Embryo and Larval"))
  
  eb <- ggplot2::element_blank()
  
  g <- ggplot2::ggplot(data = dat$datasets, mapping = ggplot2::aes(x = .data$tstart, y = .data$name, xend = .data$tend)) +
    ggplot2::geom_segment(data = dat$datasets, ggplot2::aes(yend = .data$name, col = .data$name, size = 1.5), show.legend = F) +
    ggplot2::geom_text(data = dat$datasets, ggplot2::aes(col = .data$name, label = .data$name, size = 2), 
                       fontface = "bold", vjust = "bottom", hjust = "left", nudge_y = .1,
                       show.legend = F) +
    ggplot2::geom_text(data = lbs, ggplot2::aes(label = .data$tunit), 
                       x = Inf, y = -Inf, hjust = 1.5, vjust = -1, inherit.aes = F) +
    
    ggplot2::geom_segment(data = dat$devstages, ggplot2::aes(size = 1, y = "DevStage", yend = "DevStage"), 
                          color = rep(c("grey50", "grey90"), length.out = nrow(dat$devstages)), show.legend = F) +
    ggplot2::geom_text(data = dat$devstages, ggplot2::aes(y = "DevStage", label = .data$name), size = 3, 
                       fontface = "bold", vjust = "bottom", hjust = "left", nudge_y = rep(c(.1, -.1, -.2), l = nrow(dat$devstages)), 
                       color = rep(c("black", "grey50"), length.out = nrow(dat$devstages)),
                       show.legend = F) +
    ggplot2::scale_x_continuous("time (log scale)", trans = "log1p", breaks = c(dat$devstages$tstart[1], dat$devstages$tend)) + 
    
    ggplot2::facet_wrap(~.data$tunit, scales = "free", nrow = 2) +
    ggplot2::theme_classic() + #ggplot2::xlab("time") + 
    ggplot2::theme(strip.background = eb, strip.text = eb, 
                   axis.title.y = eb, axis.text.y = eb) 
  print(g)
  return(g)
}