R/StatManhattan.R

In mcanouil/mctools: Mickaël Canouil's tools

# library(data.table)
# library(ggplot2)
# library(scales)

fortify.manhattan <- function(data, x, y, group) {
  map_chro <- c(seq(22), "X", "Y", "X", "Y")
  names(map_chro) <- c(seq(24), "X", "Y")

  `:=` <- data.table::`:=`

  out <- data.table::as.data.table(data)
  data.table::setnames(out, c(x, y, group), c("x_pos", "y_pval", "x_chr"))
  out[, x_chr := as.character(x_chr)]
  out[, x_chr := map_chro[gsub("^chr", "", x_chr, ignore.case = TRUE)]]
  out[, x_chr := factor(x_chr, levels = intersect(c(seq(22), "X", "Y"), x_chr))]
  out[, x_pos := as.double(x_pos)]
  out[order(x_chr, x_pos)]
  out[, x_pos := scales::rescale(x = x_pos, to = c(-0.4, 0.4)), by = "x_chr"]
  out[, x_pos := x_pos + as.integer(x_chr)]
  data.table::setnames(out, c("x_pos", "y_pval", "x_chr"), c("x", "y", "group"))
  out[]
}

StatManhattan <- ggplot2::ggproto("StatManhattan", ggplot2::Stat,
  required_aes = c("x", "y", "group"),
  setup_data = function(data, params) {
    fortify.manhattan(data, "x", "y", "group")
  },
  compute_layer = function(data, scales, params) {
    data
  }
)