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Get Started with glydraw

glydraw.Rmd

glydraw draws SNFG glycan cartoons from glycan structure text or glyrepr::glycan_structure() objects. The main workflow is:

  1. Draw one glycan with draw_cartoon().
  2. Save one cartoon with save_cartoon().
  3. Export many cartoons with export_cartoons().

This vignette uses IUPAC-condensed strings because they are compact and easy to copy into examples.

Draw one glycan

The first argument, structure, is the glycan to draw. It can be a character string in a notation supported by glyparse::auto_parse(), or a glyrepr::glycan_structure() value.

n_core <- "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"

draw_cartoon(n_core)

Drawing parameters

draw_cartoon() returns a ggplot2 object with class glydraw_cartoon. You can print it directly, pass it to save_cartoon(), or add normal ggplot2 layers when needed.

show_linkage

show_linkage controls whether glycosidic linkage annotations are shown. Substituent annotations are always shown.

draw_cartoon(n_core, show_linkage = FALSE)

orient

orient controls the overall direction of the cartoon. Use "H" for the default horizontal layout or "V" for a vertical layout.

draw_cartoon(n_core, orient = "V")

fuc_orient

fuc_orient controls how Fuc triangles are rotated. The default, "flex", points non-reducing Fuc residues toward their rendered linkage direction. Use "up" when every Fuc triangle should point upward.

fucosylated <- "Gal(b1-3)[Fuc(a1-4)]GlcNAc(b1-"

draw_cartoon(fucosylated, fuc_orient = "flex")

draw_cartoon(fucosylated, fuc_orient = "up")

red_end

red_end controls the reducing-end annotation. The default "" draws the standard reducing-end line. Use "~" for a wavy reducing end, or pass any other string to draw that string at the reducing end.

draw_cartoon(n_core, red_end = "~")

draw_cartoon(n_core, red_end = "R")

edge_linewidth and node_linewidth

edge_linewidth controls linkage line width. node_linewidth controls the border width of residue symbols.

draw_cartoon(
  n_core,
  edge_linewidth = 1.4,
  node_linewidth = 0.4
)

node_size

node_size is a multiplier for the default residue-symbol size. The default is 1. Larger nodes keep the same cartoon layout but draw larger symbols.

draw_cartoon(n_core, node_size = 1.2)

draw_cartoon(n_core, node_size = 1.6)
#> Warning: Linkage annotations are hidden because `node_size` is larger than 1.2.
#> ℹ Set `show_linkage = FALSE` to silence this warning, or use a smaller
#>   `node_size`.

Very large symbols can overlap, so values larger than 2 are rejected. Linkage annotations are hidden with a warning when the requested node size leaves too little annotation space.

colors

colors is an optional named character vector for overriding monosaccharide fill colors. Names must be supported monosaccharide names. Only the names you provide are changed; all other monosaccharides keep their default SNFG colors.

draw_cartoon(
  n_core,
  colors = c(Man = "#4DAF4A", GlcNAc = "#377EB8")
)

highlight

highlight marks selected residue nodes. It is available when structure is a glyrepr::glycan_structure() object. Node indices match the monosaccharide order in the printed IUPAC-condensed structure.

highlight_glycan <- glyrepr::as_glycan_structure(
  "Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-"
)

draw_cartoon(highlight_glycan, highlight = c(1, 3))

Save one cartoon

Use save_cartoon() when you already have one cartoon object.

cartoon <- draw_cartoon(n_core, red_end = "~")
outfile <- file.path(tempdir(), "n-core.png")

save_cartoon(cartoon, outfile, scale = 2)
outfile
#> [1] "/tmp/Rtmpl7JAwq/n-core.png"

glydraw does not expose separate width and height controls because each cartoon has a natural size calculated from its glycan structure. scale preserves the aspect ratio and relative symbol sizes.

Export many cartoons

Use export_cartoons() to draw and save a vector of glycans in one call. The input can be a character vector or a glyrepr::glycan_structure() vector.

glycans <- c(
  core = "Man(a1-3)Man(b1-4)GlcNAc(b1-",
  antenna = "Gal(b1-4)GlcNAc(b1-",
  fucosylated = "Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-"
)

outdir <- file.path(tempdir(), "glydraw-cartoons")
suppressMessages(
  cartoons <- export_cartoons(
    glycans,
    outdir,
    file_ext = "png",
    scale = 1.5,
    red_end = "~",
    node_size = 1.1
  )
)

list.files(outdir)
#> [1] "antenna.png"     "core.png"        "fucosylated.png"

export_cartoons() creates dirname when needed and returns the list of cartoons invisibly. File names come from vector names when present. Unnamed inputs use sanitized IUPAC-condensed structure text as file names, and duplicate names are made unique.