make_volcano.R

#' generate volcano plots with EnanchedVolcano
#' @table a tibble in the format limma::topTable
#' @coef the coeffincient to be filtered
#' @img_dir save image to directory
#' @fdr_threshold the max FDR allowed to color targets
#' @save bool (def. TRUE)
make_volcano <- function(table, coef, img_dir, fdr_threshold=0.1, save=TRUE) {
  # filter for coefficient
  table %>%
    dplyr::filter(coeff == coef) -> tmp
  # set title
  title = glue::glue("{coef} | candidate biomarkers")
  # set filename
  img_filename = glue::glue("{coef}.volcano.png")
  # set imgpath
  imgpath = fs::path(img_dir, img_filename)
  # set lables to show
  show_lab = tmp %>% 
    # filter by FRD
  dplyr::filter(adj.P.Val <= fdr_threshold) %>%
    # pull labels
  dplyr::pull("EntrezGeneSymbol")
  # sett total names
  names_lab = tmp %>% 
    dplyr::pull(EntrezGeneSymbol)
  # do volcano with EnhancedVolcano
  EnhancedVolcano::EnhancedVolcano(
    toptable = tmp,
    title=title,
    subtitle="",
    lab = names_lab,
    x = 'logFC',
    y = 'P.Value',
    selectLab = show_lab,
    pCutoffCol = "adj.P.Val",
    pCutoff = fdr_threshold,
    FCcutoff = 0,
    legendLabels = c("NS", "NS", "NS", "sign"),
    col = c("grey", "grey", "grey", "red")
    ) -> figure_
  if (save) {
    # set filename
    img_filename = glue::glue("{coef}.volcano.png")
    # set imgpath
    imgpath = fs::path(img_dir, img_filename)
    ggplot2::ggsave(imgpath, plot=figure_)
  }
  return(figure_)
}