R/draw_volcano.R

In mcanouil/mctools: Mickaël Canouil's tools

# library(data.table)
# library(ggplot2)
# library(ggtext)
# devtools::source_gist("d7cbc59a7fcbb6d231f432801ec7aa19") # pval_trans)

draw_volcano <- function(
  data, x, y,
  label_x = "Fold-Change (log<sub>2</sub>)",
  label_y = "P-value",
  alpha = 0.05
) {
  data <- data.table::as.data.table(data)#[, .SD, .SDcols = c(x, y)]
  data.table::setnames(data, y, "pvalue", skip_absent = TRUE)
  ggplot2::ggplot(data) +
    ggplot2::aes(x = .data[[x]], y = .data[["pvalue"]], colour = abs(.data[[x]])) +
    ggplot2::geom_vline(xintercept = 0, linetype = 2) +
    ggplot2::geom_point(size = 0.60) +
    ggplot2::scale_colour_viridis_c(trans = "sqrt", limits = c(0, NA)) +
    ggplot2::labs(x = label_x, y = label_y) +
    ggplot2::theme(legend.position = "none") +
    ggplot2::annotate(
      geom = "rect",
      xmin = -Inf, xmax = Inf, ymin = 1, ymax = alpha,
      fill = "firebrick", alpha = 0.2, colour = NA
    ) +
    ggplot2::geom_hline(yintercept = alpha, linetype = 2, colour = "firebrick") +
    ggplot2::scale_y_continuous(
      trans = pval_trans(alpha = alpha, md = TRUE, colour = "firebrick"),
      expand = ggplot2::expansion(mult = c(0, 0.2)),
      limits = c(1, NA)
    )
}