Draw a Symbol Nomenclature For Glycan (SNFG)

Usage

draw_cartoon(
  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
)

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.

Value

a ggplot2 object

Examples

if (FALSE) { # \dontrun{
draw_cartoon("Gal(b1-3)GalNAc(a1-")
} # }