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 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

See also

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")