glycanGrob: Construct a glycan grob

In glydraw: Draw Beautiful Symbol Nomenclature for Glycans

Construct a glycan grob

Description

glycanGrob() prepares the complete drawing specification for one glycan as a grid grob. It is the low-level drawing primitive used by draw_cartoon().

Usage

glycanGrob(
  structure,
  ...,
  show_linkage = TRUE,
  orient = c("H", "V"),
  fuc_orient = c("flex", "up"),
  red_end = "",
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  colors = NULL,
  highlight = NULL,
  style = NULL
)

Arguments

structure	A glyrepr::glycan_structure() scalar, or a string of any glycan structure text nomenclatures supported by glyparse::auto_parse().
...	Ignored.
show_linkage	Show glycosidic linkage annotations or not. Default is TRUE. Substituent annotations are always shown.
orient	The orientation of glycan structure. "H" for horizontal, "V" for vertical. Default is "H"
fuc_orient	Fuc-like triangle orientation. "flex" points non-reducing Fuc-like residues toward their rendered linkage direction, while "up" draws all Fuc-like triangles pointing upward. Reducing-end Fuc-like residues always point upward. Defaults to "flex".
red_end	Reducing-end annotation. The default "" keeps the current reducing-end line. Use "~" to add a wavy reducing end, or any other string to draw that string at the reducing end.
edge_linewidth	Numeric scalar controlling the linewidth of linkage lines. Defaults to the current value, 0.8.
node_linewidth	Numeric scalar controlling the linewidth of node borders. Defaults to the current value, 0.8.
node_size	Numeric scalar used as a multiplier for the default node size. Defaults to 1, which keeps the current size. Linkage annotations are moved farther from larger nodes, and are hidden with a warning when node_size is too large to leave enough annotation space. Values larger than 2 are rejected because residues overlap.
colors	Optional named character vector of custom monosaccharide fill colors. Names must be supported monosaccharide names, such as "Gal" or "GlcNAc". User-provided colors overwrite the default SNFG colors, while unprovided monosaccharides keep their default colors. Defaults to NULL.
highlight	An integer vector specifying the node indices to highlight. This argument is applicable only when structure is a glyrepr::glycan_structure(). Note that for a glyrepr::glycan_structure(), the node indices correspond exactly to the monosaccharides in its printed IUPAC nomenclature. For example, given glyrepr::as_glycan_structure("Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-"), setting highlight = c(1, 3) will highlight the "Gal" and "GalNAc" nodes.
style	A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

Value

A glycanGrob object inheriting from grid::gTree().

Examples

grob <- glycanGrob("Gal(b1-3)GalNAc(a1-")
grid::grid.draw(grob)

glydraw documentation built on July 25, 2026, 9:06 a.m.