R/geom_subgene_label.R

In wilkox/gggenes: Draw Gene Arrow Maps in 'ggplot2'

#' A 'ggplot2' geom to add text labels to subgenes
#'
#' `geom_subgene_label()` can be used to add a text label to subgenes drawn
#' with `geom_subgene_arrow()`.
#'
#' `geom_subgene_label()` uses the 'ggfittext' package to fit text to genes.
#' All text drawing options available in `ggfittext::geom_fit_text()` (growing,
#' reflowing, etc.) are also available here. For full details on how these
#' options work, see the documentation for `ggfittext::geom_fit_text()`.
#'
#' Standard 'ggplot2' aesthetics for text are supported (see Aesthetics.)
#'
#' @param padding.x,padding.y `grid::unit()` object, giving horizontal or
#' vertical padding around the text. Defaults to 1 mm and 0.1 lines
#' respectively.
#' @param align Where inside the subgene to place the text label. Default is
#' 'centre'; other options are 'left' and 'right'.
#' @param min.size Minimum font size, in points. If provided, text that would
#' need to be shrunk below this size to fit inside the subgene will not be
#' drawn. Defaults to 4 pt.
#' @param grow If `TRUE`, text will be grown as well as shrunk to fill the
#' subgene.
#' @param reflow If `TRUE`, text will be reflowed (wrapped) to better fit the
#' subgene.
#' @param height `grid::unit()` object giving the maximum height of the text.
#' Defaults to 3 mm, which is the default height of gene arrows (and therefore
#' of subgenes) drawn with `geom_gene_arrow()`.
#' @param mapping,data,stat,position,na.rm,show.legend,inherit.aes,... Standard
#' geom arguments as for `ggplot2::geom_text()`.
#' 
#' @section Aesthetics:
#'
#' -  xsubmin,xsubmax (start and end of the subgene; required)
#' -  y (molecule; required)
#' -  colour
#' -  size
#' -  alpha
#' -  family
#' -  fontface
#' -  angle
#'
#' @export
geom_subgene_label <- function(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  padding.x = grid::unit(1, "mm"),
  padding.y = grid::unit(0.1, "lines"),
  align = "centre",
  min.size = 4,
  grow = F,
  reflow = F,
  height = grid::unit(3, "mm"),
  ...
) {
  ggplot2::layer(
    data = data,
    mapping = mapping,
    stat = stat,
    geom = GeomSubgeneLabel,
    position = position,
    show.legend = show.legend,
    inherit.aes = inherit.aes,
    params = list(
      na.rm = na.rm,
      padding.x = padding.x,
      padding.y = padding.y,
      align = align,
      min.size = min.size,
      grow = grow,
      reflow = reflow,
      height = height,
      ...
    )
  )
}

#' GeomSubgeneLabel
#' @noRd
#' @import grid
#' @import ggfittext
GeomSubgeneLabel <- ggplot2::ggproto(
  "GeomSubgeneLabel",
  ggplot2::Geom,
  required_aes = c("xsubmin", "xsubmax", "y", "label"),
  default_aes = ggplot2::aes(
    colour = "black",
    size = 18,
    alpha = 1,
    family = "",
    fontface = 1,
    angle = 0,
    fill = "white",
    lineheight = 0.9
  ),

  draw_key = ggplot2::draw_key_text,

  draw_panel = function(
    data,
    panel_scales,
    coord,
    padding.x = grid::unit(1, "mm"),
    padding.y = grid::unit(1, "mm"),
    min.size = 4,
    grow = FALSE,
    reflow = FALSE,
    align = "centre",
    height = grid::unit(3, "mm"),
    subgroup = NA
  ) {

    # Detect coordinate system
    coord_system <- get_coord_system(coord)
    if (coord_system == "flip") {
      data$angle <- data$angle + 90
    }

    # Convert aesthetic names
    data$xmin <- data$xsubmin
    data$xmax <- data$xsubmax
    data$xsubmin <- NULL
    data$xsubmax <- NULL

    # Transform data to panel scales
    data <- coord$transform(data, panel_scales)

    # Check the value of 'align'
    if (! align %in% c("left", "centre", "center", "middle", "right")) {
      cli::cli_abort("`align` must be one of `left`, `centre`, `center`, `middle` or `right`")
    }

    # Use ggfittext's fittexttree to draw the text
    if (coord_system == "flip") {
      gt <- grid::gTree(
        data = data,
        padding.x = padding.x,
        padding.y = padding.y,
        place = align,
        min.size = min.size,
        grow = grow,
        reflow = reflow,
        cl = "fittexttree",
        width = height,
        fullheight = TRUE
      )
    } else if (coord_system == "cartesian") {
      gt <- grid::gTree(
        data = data,
        padding.x = padding.x,
        padding.y = padding.y,
        place = align,
        min.size = min.size,
        grow = grow,
        reflow = reflow,
        cl = "fittexttree",
        height = height,
        fullheight = TRUE
      )
    } else {
      cli::cli_abort("Don't know how to draw in this coordinate system")
    }
    gt$name <- grid::grobName(gt, "geom_subgene_label")
    gt
  }
)