R/geom_bar-method.R

In ggbio: Visualization tools for genomic data

setGeneric("geom_bar", function(data, ...) standardGeneric("geom_bar"))

setMethod("geom_bar", "ANY", function(data, ...){
  ggplot2::geom_bar(data  = data, ...)
})
## alignment should be convenient toggle with chevron...
setMethod("geom_bar", "GRanges", function(data,..., xlab, ylab, main){

  args <- list(...)
  args.aes <- parseArgsForAes(args)
  args.non <- parseArgsForNonAes(args)
  args.facets <- subsetArgsByFormals(args, facet_grid, facet_wrap)
  facet <- .buildFacetsFromArgs(data, args.facets)
  if(length(data)){
    if(!"y" %in% names(args.aes)){
      if("score" %in% colnames(values(data))){
        message("use score as y by default")
        args.aes$y <- as.name("score")
      }else{
        stop("missing y values in aes(), or please provide a column named 'score'")
      }
    }
    .y <- quo_name(args.aes$y)
    ylab <- .y
    args.aes <- args.aes[names(args.aes) != "y"]
    
    args.aes$xmin <- as.name("start")
    args.aes$xmax <- as.name("end")
    args.aes$ymin <- 0
    args.aes$ymax <- as.name(.y)
    aes.res <- do.call(aes, args.aes)
    p <- list(do.ggcall(geom_rect, c(list(data = mold(data)),
                                     list(aes.res),
                                     args.non)))

  }else{
    p <- NULL
  }
  p <- c(p, list(facet))
  if(missing(xlab)) 
    xlab <- ""
  p <- c(p, list(ggplot2::xlab(xlab)))
  if(!missing(ylab))
    p <- c(p, list(ylab(ylab)))
  if(!missing(main))
    p <- c(p, list(labs(title = main)))
  p
})