A 'ggplot2' geom to draw subgene segments of gene arrows

Source: R/geom_subgene_arrow.R

geom_subgene_arrow() draws subgenes segments within gene arrows drawn with geom_gene_arrow().

geom_subgene_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

The start and end locations of the subgene are given with the xsubmin and xsubmax aesthetics. geom_subgene_arrow() requires some information about the 'parent' gene, provided with the same aesthetics used for geom_gene_arrow(): start and end locations of the 'parent' gene with the xmin and xmax aesthetics, the molecule with the y aesthetic, and optionally the direction with the forward aesthetic. If the geometry of the parent gene has been changed with arrowhead_width, arrowhead_height or arrow_body_height, identical parameters should be given to geom_subgene_arrow().

Aesthetics

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

  • xsubmin,xsubmax (start and end of subgene segment). Should be consistent with xmin/xmax

  • y (molecule)

  • forward (if FALSE, or coercible to FALSE, 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)) +
geom_gene_arrow() +
geom_subgene_arrow(data = example_subgenes,
      ggplot2::aes(xmin = start, xmax = end, xsubmin = from, xsubmax = to,
                   y = molecule, fill = gene)) +
ggplot2::facet_wrap(~ molecule, scales = "free")