gggenes (version 0.6.0)

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

Description

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

Usage

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.

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

• linewidth (the former size aesthetic has been deprecated and will be removed in future versions)

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().

See Also

geom_gene_arrow(), geom_subgene_label()

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")