Export all glycan structures to figures

Draw and save one cartoon for each glycan structure in x.

Usage

export_cartoons(
  x,
  dirname,
  ...,
  file_ext = "png",
  dpi = 300,
  scale = 1,
  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
)

Arguments

x: A glyrepr::glycan_structure() vector, or a character vector of any glycan structure text nomenclatures supported by glyparse::auto_parse().
dirname: Directory name to save the cartoons. If it does not exist, it is created.
...: Ignored.
file_ext: File extension supported by ggplot2::ggsave(). Defaults to "png".
dpi: Deprecated and ignored. Use scale to change the output size.
scale: Numeric output-size multiplier passed to save_cartoon().
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.

Value

The function returns the list of cartoons implicitly.

File names

IUPAC-condensed nomenclatures are used as file names. If x is a named character vector or named glyrepr::glycan_structure() vector, the vector names are used as file names.

Why not `width` and `height`?

The familiar ggplot2::ggsave() interface uses width, height, and dpi because ordinary ggplot2 plots are drawn into a user-chosen device size. glydraw cartoons are different: the natural width and height are calculated from the glycan structure so residues, linkages, labels, and borders stay comparable across different glycans. If users supplied arbitrary width and height, glydraw would either distort that structure-derived layout or need to guess how to reconcile one requested size with the other.

dpi is also not the right control here because changing it alters how point- and inch-based ggplot2 elements are rasterized relative to the fixed cartoon canvas. glydraw therefore keeps an internal fixed design scale and uses scale as a single multiplier for the final pixel dimensions. This preserves the cartoon's aspect ratio and relative appearance while still allowing larger or smaller output files.

Examples