A 'ggplot2' geom to draw point genetic features

Source: R/geom_feature.R

geom_feature() draws lines to indicate the positions of point genetic features, for example restriction sites, origins of replication or transcription start sites.

geom_feature(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  feature_height = unit(3, "mm"),
  feature_width = unit(3, "mm"),
  arrowhead_width = unit(2, "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 features are not likely to share any plot aesthetics other than y.

feature_height

grid::unit() object giving the height of a feature above the molecule line. Can be set as a negative value to draw features below the line. Defaults to 3 mm.

feature_width

grid::unit() object giving the width of a feature (distance from the elbow to the tip of the arrow). Only relevant for oriented features. Defaults to 3 mm.

arrowhead_width

grid::unit() object giving the width of the arrowhead indicating the direction of an oriented feature. Only relevant for oriented features. Defaults to 2 mm.

Details

Features are drawn as vertical lines extending from the horizontal line representing the molecule. The position of the feature is expressed with the x aesthetic. Optionally, the forward aesthetic can be used to specific an orientation for the feature (e.g. the direction of transcription), in which case an angled arrowhead will be added. The forward aesthetic assumes that the x-axis is oriented in the normal direction, i.e. increasing from left to right; if it is not, the values in forward will need to be inverted manually.

Aesthetics

  • x (required; position of the feature)

  • y (required; molecule)

  • forward (optional; if TRUE, or a value coercible to TRUE, the feature will be drawn with an arrowhead pointing right, if FALSE, pointing left, if NA, the feature will be drawn as a vertical line)

  • alpha

  • colour

  • linetype

  • size

Examples


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