Use glycan cartoons as axis labels — scale_x

scale_x_glycan() and scale_y_glycan() are discrete position scales that replace text tick labels with compact glycan cartoons. Mapped discrete values and values returned by the scale's labels argument may be glycan structure strings supported by glyparse::auto_parse() or glyrepr::glycan_structure() vectors. X-axis cartoons are vertical and bottom-aligned by default, while y-axis cartoons are horizontal and right-aligned by default. The cartoon orientation and alignment adapt to the displayed axis, including when the axes are swapped by ggplot2::coord_flip().

Usage

scale_x_glycan(
  name = ggplot2::waiver(),
  ...,
  palette = seq_len,
  expand = ggplot2::waiver(),
  position = "bottom",
  sec.axis = ggplot2::waiver(),
  continuous.limits = NULL,
  size = 0.4,
  angle = 0,
  hjust = hjust_red_end(),
  vjust = 0,
  nudge_x = 0,
  nudge_y = 0,
  show_linkage = TRUE,
  style = style_glydraw(),
  red_end = NULL,
  orient = NULL
)

scale_y_glycan(
  name = ggplot2::waiver(),
  ...,
  palette = seq_len,
  expand = ggplot2::waiver(),
  position = "left",
  sec.axis = ggplot2::waiver(),
  continuous.limits = NULL,
  size = 0.4,
  angle = 0,
  hjust = 1,
  vjust = vjust_red_end(),
  nudge_x = 0,
  nudge_y = 0,
  show_linkage = TRUE,
  style = style_glydraw(),
  red_end = NULL,
  orient = NULL
)

Arguments

name: The name of the scale, displayed as the axis title. Use NULL to remove the title.
...: Arguments passed to ggplot2::scale_x_discrete() or ggplot2::scale_y_discrete(), including breaks and labels.
palette: A palette function that returns discrete position values.
expand: Expansion applied to the discrete position scale.
position: Position of the axis.
sec.axis: A secondary axis specification.
continuous.limits: Continuous limits used to position the discrete scale.
size: Positive scalar that uniformly scales each axis-label cartoon. Defaults to 0.4.
angle: Rotation in degrees applied to each axis-label cartoon, independently of the cartoon orientation. Defaults to 0.
hjust: Horizontal justification. When omitted, cartoons on a top or bottom axis with a vertical orientation use hjust_red_end(). Cartoons on a left or right axis with a horizontal orientation use 1 or 0, respectively. Other position-orientation combinations use 0.5.
vjust: Vertical justification. When omitted, cartoons on a top or bottom axis with a vertical orientation use 0. Cartoons on a left or right axis with a horizontal orientation use vjust_red_end(). Other position-orientation combinations use 0.5.
nudge_x: Horizontal adjustment of each cartoon, in millimetres. Positive values move cartoons to the right. When this moves cartoons toward or away from a y-axis title, the title moves with them to preserve the gap. Defaults to 0.
nudge_y: Vertical adjustment of each cartoon, in millimetres. Positive values move cartoons upward. When this moves cartoons toward or away from an x-axis title, the title moves with them to preserve the gap. Defaults to 0.
show_linkage: Whether to show glycosidic linkage annotations inside the cartoons. Defaults to TRUE.
style: A style_glydraw() object that controls the cartoons' visual appearance.
red_end: Reducing-end annotation. NULL, the default, uses red_end from style. A non-NULL value overrides style$red_end.
orient: Glycan drawing orientation. NULL, the default, selects the orientation from the displayed axis position: "up" for "bottom" or "top", "left" for "left", and "right" for "right".

Value

A ggplot2 discrete position scale.

Examples

glycans <- data.frame(
  structure = c(
    "Gal(b1-3)GalNAc(a1-",
    "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-"
  ),
  abundance = c(12, 8)
)

ggplot2::ggplot(glycans, ggplot2::aes(x = structure, y = abundance)) +
  ggplot2::geom_col() +
  scale_x_glycan()