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A 'ggplot2' geom to draw transcription terminators

Source: R/geom_terminator.R
geom_terminator.Rd

geom_terminator() draws a 'T-shaped' glyph representing the position of a transcription terminator.

Usage

geom_terminator(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  terminator_height = unit(3, "mm"),
  terminator_width = unit(3, "mm"),
  ...
)

Arguments

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

As standard for ggplot2. inherit.aes is set to FALSE by default, as terminators are not likely to share any plot aesthetics other than y.

terminator_height

grid::unit() object giving the height of the vertical 'pillar' of the terminator glyph above the molecule line. Can be set as a negative value to draw terminators below the line. Defaults to 3 mm.

terminator_width

grid::unit() object giving the width of the horizontal 'beam' of the terminator glyph. Defaults to 3 mm.

Aesthetics

  • x (required; position of the terminator)

  • y (required; molecule)

  • alpha

  • color

  • linetype

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

Note that, unlike geom_gene_arrow() and ggplot2 convention, linewidth in geom_terminator() is expressed in points rather than millimetres, with a default value of 1. This inconsistency is retained for backwards compatibility, and will be reconciled when these point-feature geoms are superseded in gggenes 1.0.0.

See also

geom_terminator_label(), geom_feature()

Examples


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