Plot a glycan biosynthesis network — autoplot.glyenzy_biosynthesis

autoplot.glyenzy_biosynthesis_network() draws the typed networks returned by trace_biosynthesis(), trace_biosynthesis_virtual(), path_biosynthesis(), and path_biosynthesis_virtual(). A layered DAG layout determines the node positions while accounting for converging biosynthesis routes. Parallel enzyme names are combined on one reaction edge.

Usage

# S3 method for class 'glyenzy_biosynthesis_network'
autoplot(
  object,
  show_enzyme = TRUE,
  size = 0.4,
  node_gap = 0.25,
  level_gap = 0.6,
  width = 6,
  height = 6,
  units = c("in", "cm", "mm"),
  show_linkage = FALSE,
  orient = c("left", "right", "up", "down"),
  color_edge = FALSE,
  enzyme_label_style = c("condensed", "full"),
  highlight_target = NULL,
  ...
)

Arguments

object: A glyenzy_biosynthesis_network object returned by a biosynthesis function.
show_enzyme: Logical. Whether to label reaction edges with enzyme or virtual-enzyme names. Labels that would be too small to render after panel fitting are hidden with a warning.
size: Positive numeric whole-cartoon scale multiplier passed to glydraw::geom_node_glycan(). Defaults to 0.4.
node_gap: Non-negative physical clearance, in inches, between glycan nodes at the same rank.
level_gap: Non-negative physical clearance, in inches, between adjacent ranks. Increase this when enzyme labels are unusually long.
width, height: Positive, finite figure dimensions. Networks larger than the available figure are scaled proportionally, while smaller networks retain their natural size and are centered in the figure.
units: Units for width and height. One of "in" (the default), "cm", or "mm".
show_linkage: Logical. Whether glycan linkage annotations are shown. Defaults to FALSE for a compact network.
orient: Glycan drawing orientation passed to glydraw::geom_node_glycan(). One of "left", "right", "up", or "down"; the default is "left".
color_edge: Logical. Whether reaction edges and enzyme labels use the SNFG color of the residue added by each reaction. Defaults to FALSE, which draws them in dark grey. Concrete and virtual reactions use solid and dashed lines, respectively, in both modes. Reactions without one unambiguous added residue remain dark grey.
enzyme_label_style: How parallel enzymes on one reaction edge are labeled. "condensed" (the default) groups names with the same prefix and terminal number, for example, "B4GALT1/2/3, B3GALT3/4". "full" keeps complete names separated by " / ".
highlight_target: Logical or NULL. When TRUE, target glycans are drawn normally and all other glycans are semi-transparent. The default, NULL, highlights targets in multi-target networks but not in single-target networks. Reaction edges and enzyme labels are unchanged. This argument cannot be TRUE for networks returned by path_biosynthesis() or path_biosynthesis_virtual().
...: Additional glycan appearance arguments accepted by glydraw::glycanGrob(), such as node_size, colors, or style.

Value

A ggraph/ggplot object with a fixed-size, collision-aware layered panel centered in the requested figure dimensions.

Details

Glycan dimensions are measured before the network is laid out. Nodes at the same rank are separated by their rendered bounds, while rectangular edge caps stop arrows outside the source and target glycans. The plot uses a fixed-size panel inside a requested figure canvas so these clearances remain physical rather than changing with the coordinate range.

Concrete enzyme reactions use solid edge shafts, while virtual enzyme reactions use dashed shafts; arrowheads remain solid in both cases. This convention is documented rather than repeated in an in-plot legend.

Figure size

width, height, and units describe the complete base figure returned by this method. Use the same dimensions with ggplot2::ggsave() or the corresponding knitr/Quarto figure options. Titles, legends, or margins added after this method returns may require additional output space.

Examples

if (FALSE) { # \dontrun{
network <- trace_biosynthesis_virtual(
  "GlcNAc(b1-4)Gal(b1-3)GalNAc(a1-"
)
network_plot <- ggplot2::autoplot(network, width = 8, height = 5)
ggplot2::ggsave(
  "biosynthesis-network.png",
  network_plot,
  width = 8,
  height = 5,
  units = "in"
)
} # }