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Glycan drawing styles

Source: R/style-glydraw.R
style_glydraw.Rd

Style constructors collect the rendering options shared by glydraw's standalone drawings, grobs, ggplot2 layers, guides, and glycan scales. style_glydraw() provides glydraw's default appearance, while the other constructors provide presets matching common glycan-drawing conventions. Supply a returned style with style = to reuse its visual specification.

Usage

style_glydraw(
  fuc_orient = "flex",
  red_end = "",
  red_end_length = 0.6,
  red_end_size = 6,
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  font_family = "",
  colors = glydraw_colors()
)

style_glygen(
  fuc_orient = "flex",
  red_end = "~",
  red_end_length = 1,
  red_end_size = 6,
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  font_family = "arial",
  colors = glydraw_colors()
)

style_snfg(
  fuc_orient = "up",
  red_end = "",
  red_end_length = 1,
  red_end_size = 6,
  edge_linewidth = 1.5,
  node_linewidth = 0.8,
  node_size = 1.15,
  font_family = "arial",
  colors = glydraw_colors()
)

style_glycoworkbench(
  fuc_orient = "flex",
  red_end = "~",
  red_end_length = 1,
  red_end_size = 6,
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  font_family = "arial",
  colors = c(glyWhite = "#FFFFFF", glyBlue = "#0000F0", glyGreen = "#5AC54B", glyYellow =
    "#FFFF54", glyOrange = "#F7EAD7", glyPink = "#FFFFFF", glyPurple = "#B726C1",
    glyLightBlue = "#EDFEFF", glyBrown = "#8F663B", glyRed = "#E53222")
)

Arguments

fuc_orient

Fuc-like triangle orientation: "flex" or "up".

red_end

Reducing-end annotation. Use "~" for a wave, any other string for custom text, or tag one amino-acid site as "ABC<site>D</site>EFG". Ignored when red_end_length is 0.

red_end_length

Length of the reducing-end line in plot coordinate units. Set to 0 to omit the line and any red_end wave or custom text while retaining the axis-aligned core anomer annotation.

red_end_size

Size of custom text passed to red_end. The "~" wave is not affected.

edge_linewidth

Linewidth of glycosidic linkages.

node_linewidth

Linewidth of node borders.

node_size

Multiplier for the default node size.

font_family

A length-one character string naming the font family used for linkage, substituent, and reducing-end text annotations. Portable choices are "sans", "serif", and "mono". Other family names, such as installed system fonts, are graphics-device dependent. The default "" uses the graphics device's default font.

colors

A named character vector of SNFG colors in the format returned by glydraw_colors(). Names must be complete and match that palette.

Value

A glydraw_style object.

Functions

  • style_glydraw(): Use glydraw's default style.

  • style_glygen(): Use a GlyGen-style preset.

  • style_snfg(): Use a Symbol Nomenclature for Glycans preset.

  • style_glycoworkbench(): Use a GlycoWorkbench-style preset.

Examples

serif_style <- style_glydraw(font_family = "serif")
draw_cartoon("Gal(b1-3)GalNAc(a1-", style = serif_style)


draw_cartoon("Gal(b1-3)GalNAc(a1-", style = style_glygen())

draw_cartoon("Gal(b1-3)GalNAc(a1-", style = style_snfg())

draw_cartoon("Gal(b1-3)GalNAc(a1-", style = style_glycoworkbench())