A 'ggplot2' geom to draw genes as arrows

Source: R/geom_gene_arrow.R

geom_gene_arrow() draws genes as arrows, allowing gene maps to be drawn.

geom_gene_arrow(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrowhead_width = grid::unit(4, "mm"),
  arrowhead_height = grid::unit(4, "mm"),
  arrow_body_height = grid::unit(3, "mm"),
  ...
)

Arguments

mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...

As standard for ggplot2.

arrowhead_width

grid::unit() object giving the width of the arrowhead. Defaults to 4 mm. If the gene is drawn smaller than this width, only the arrowhead will be drawn, compressed to the length of the gene.

arrowhead_height

grid::unit() object giving the height of the arrowhead. Defaults to 4 mm.

arrow_body_height

grid::unit() object giving the height of the body of the arrow. Defaults to 3 mm.

Details

This geom draws genes as arrows along a horizontal line representing the molecule. The start and end locations of the gene are expressed with the xmin and xmax aesthetics, while the molecule can be specified with the y aesthetic. Optionally, an additional forward aesthetic can be used to reverse the orientation of some or all genes from that implied by xmin and xmax.

Unless the plot is faceted with a free x scale, all the molecules will share a common x axis. This means that if the locations are very different across different molecules, the genes might appear very small and squished together with a lot of unnecessary empty space. To get around this, either facet the plot with scales = "free_x", or normalise the gene locations if their exact locations are not important.

See make_alignment_dummies() for a method to align genes between molecules.

Aesthetics

  • xmin,xmax (start and end of the gene; will be used to determine gene orientation)

  • y (molecule)

  • forward (if any value that is not TRUE, or coercible to TRUE, the gene arrow will be drawn in the opposite direction to that determined by xmin and xmax)

  • alpha

  • colour

  • fill

  • linetype

  • size

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free")