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("left", "right", "up", "down"),
  style = style_glydraw(),
  red_end = 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: Direction in which the glycan extends from its reducing end: one of "left", "right", "up", or "down". Defaults to "left".
style: A style_glydraw() object that controls the cartoon's visual appearance.
red_end: Reducing-end annotation. NULL, the default, uses red_end from style. A non-NULL value overrides style$red_end. Ignored when style$red_end_length is 0. To annotate an amino-acid sequence, tag its single glycosite as, for example, "ABC<site>D</site>EFG".

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