Help for package glydraw

Title:

Draw Beautiful Symbol Nomenclature for Glycans

Version:

0.7.0

Description:

A 'ggplot2'-native plotting engine for drawing reproducible beautiful Symbol Nomenclature for Glycans (SNFG) glycan cartoons from glycan structure objects or text notations, with support for batch export, structural highlighting, and deep appearance customization. It follows the SNFG specification described at https://www.ncbi.nlm.nih.gov/glycans/snfg.html.

License:

MIT + file LICENSE

Suggests:

ggraph, knitr, rmarkdown, testthat (≥ 3.0.0), tibble, vdiffr

Config/testthat/edition:

Encoding:

UTF-8

RoxygenNote:

7.3.3

URL:

https://glycoverse.github.io/glydraw/, https://github.com/glycoverse/glydraw

Imports:

glyrepr (≥ 0.10.0), rlang, dplyr, ggplot2 (≥ 4.0.0), igraph, purrr, png, glyparse, cli, checkmate, scales, fs

Depends:

R (≥ 4.1)

VignetteBuilder:

knitr

BugReports:

https://github.com/glycoverse/glydraw/issues

NeedsCompilation:

Packaged:

2026-07-25 04:39:27 UTC; fubin

Author:

Bin Fu

[aut, cre, cph], Xisong Feng

[aut]

Maintainer:

Bin Fu <23110220018@m.fudan.edu.cn>

Repository:

CRAN

Date/Publication:

2026-07-25 05:00:02 UTC

glydraw: Draw Beautiful Symbol Nomenclature for Glycans

Description

Author(s)

Maintainer: Bin Fu 23110220018@m.fudan.edu.cn (ORCID) [copyright holder]

Authors:

Xisong Feng 1225774778@qq.com (ORCID)

Draw a Symbol Nomenclature For Glycan (SNFG)

Description

Draw a Symbol Nomenclature For Glycan (SNFG)

Usage

draw_cartoon(
  structure,
  ...,
  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,
  highlight = NULL,
  style = NULL
)

Arguments

structure

A glyrepr::glycan_structure() scalar, or a string of any glycan structure text nomenclatures supported by glyparse::auto_parse().

...

Ignored.

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.

highlight

An integer vector specifying the node indices to highlight. This argument is applicable only when structure is a glyrepr::glycan_structure(). Note that for a glyrepr::glycan_structure(), the node indices correspond exactly to the monosaccharides in its printed IUPAC nomenclature. For example, given glyrepr::as_glycan_structure("Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-"), setting highlight = c(1, 3) will highlight the "Gal" and "GalNAc" nodes.

style

A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

Value

a ggplot2 object

Examples

draw_cartoon("Gal(b1-3)GalNAc(a1-")

Export all glycan structures to figures

Description

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,
  style = 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

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

colors

style

A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

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

export_cartoons(
  c(
    "Man(a1-3)Man(b1-4)GlcNAc(b1-",
    "Gal(b1-4)GlcNAc(b1-"
  ),
  tempdir()
)

Draw glycans at ggplot2 positions

Description

geom_glycan() draws one glycan cartoon for each data row. Each cartoon is anchored at its mapped x and y position and retains the structure-derived dimensions and appearance used by draw_cartoon(). The optional size aesthetic scales the complete cartoon uniformly, including nodes, lines, text, and spacing, without changing their relative appearance. Like points and text, the cartoons do not expand the position scales beyond their anchor coordinates. Use scale expansion or explicit coordinate limits when the cartoons need more room around the panel edges. Unlike standalone cartoons returned by draw_cartoon(), cartoons in this layer have no output border or background.

Usage

geom_glycan(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  angle = 0,
  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,
  highlight = NULL,
  style = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by ggplot2::aes(). The x, y, and structure aesthetics are required.

data

The data to be displayed in this layer. When NULL, the default, the data is inherited from the plot data.

stat

The statistical transformation to use on the data for this layer. Defaults to "identity".

position

A position adjustment to use on the data for this layer. Defaults to "identity".

...

Other arguments passed to ggplot2::layer().

angle

Rotation in degrees. Like ggplot2::geom_text(), this can be supplied as an aesthetic or a fixed layer value. It rotates each completed cartoon around its mapped position independently of orient. Defaults to 0.

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

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

colors

highlight

style

A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

Logical. Should this layer be included in the legends?

inherit.aes

If FALSE, overrides the default aesthetics rather than combining with them.

Value

A ggplot2 layer that can be added to a ggplot2::ggplot() object.

Aesthetics

geom_glycan() understands the following aesthetics. x, y, and structure are required; the remaining aesthetics are optional:

x
y
structure, containing glycan structure strings or glyrepr::glycan_structure() values
size, an optional whole-cartoon scale multiplier that defaults to 1. Mapped values are transformed by ggplot2's size scale; use ggplot2::scale_size_identity() when the mapped values are literal multipliers. This is distinct from node_size, which changes residue size within the cartoon.
hjust, an optional horizontal justification that defaults to 0.5. Numeric 0 aligns the cartoon content's left bound with x, and 1 aligns its right bound. Use hjust_red_end() to anchor a vertical cartoon at its reducing end.
vjust, an optional vertical justification that defaults to 0.5. Numeric 0 aligns the cartoon content's bottom bound with y, including the end of a reducing-end annotation line, and 1 aligns its top bound. Use vjust_red_end() to anchor a horizontal cartoon at its reducing end.
angle, an optional rotation in degrees that defaults to 0. Rotation is applied after the cartoon is drawn, independently of orient.

Examples

glycans <- data.frame(
  x = c(1, 3),
  y = c(1, 2),
  size = c(0.7, 1.1),
  structure = c(
    "Gal(b1-3)GalNAc(a1-",
    "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-"
  )
)

ggplot2::ggplot(
  glycans,
  ggplot2::aes(
    x = .data$x,
    y = .data$y,
    structure = .data$structure,
    size = .data$size
  )
) +
  geom_glycan() +
  ggplot2::scale_size_identity() +
  ggplot2::coord_cartesian(
    xlim = c(0, 4),
    ylim = c(0, 3),
    expand = FALSE
  )

# Bottom-align a row of vertical glycans with different heights.
ggplot2::ggplot(
  glycans,
  ggplot2::aes(x = .data$x, y = 1, structure = .data$structure)
) +
  geom_glycan(orient = "V", vjust = 0)

Draw glycans as ggraph nodes

Description

geom_node_glycan() is a ggraph node layer backed by geom_glycan(). It supplies the node layout's x and y columns as the default position aesthetics and supports ggraph's filter aesthetic.

Usage

geom_node_glycan(
  mapping = NULL,
  data = NULL,
  position = "identity",
  show.legend = NA,
  ...
)

Arguments

mapping

Set of aesthetic mappings created by ggplot2::aes(). The structure aesthetic is required. The x and y aesthetics default to the node coordinates calculated by ggraph.

data

The node data to display. When NULL, the default, the layer uses the node data calculated by ggraph::ggraph().

position

A position adjustment. Defaults to "identity".

show.legend

Logical. Should this layer be included in legends?

...

Arguments passed to geom_glycan(), including fixed aesthetics and glycan rendering options.

Value

A ggplot2 layer that can be added to a ggraph::ggraph() plot.

Aesthetics

geom_node_glycan() understands the same aesthetics as geom_glycan(). structure is required, while x and y default to the node layout coordinates. It additionally supports filter, a logical aesthetic that selects which nodes are drawn.

Examples

if (requireNamespace("ggraph", quietly = TRUE)) {
  graph <- igraph::make_ring(2)
  igraph::V(graph)$glycan <- c(
    "GalNAc(a1-",
    "Gal(b1-3)GalNAc(a1-"
  )

  ggraph::ggraph(graph, layout = "linear") +
    ggraph::geom_edge_link() +
    geom_node_glycan(ggplot2::aes(structure = .data$glycan))
}

Construct a glycan grob

Description

glycanGrob() prepares the complete drawing specification for one glycan as a grid grob. It is the low-level drawing primitive used by draw_cartoon().

Usage

glycanGrob(
  structure,
  ...,
  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,
  highlight = NULL,
  style = NULL
)

Arguments

structure

A glyrepr::glycan_structure() scalar, or a string of any glycan structure text nomenclatures supported by glyparse::auto_parse().

...

Ignored.

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

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

colors

highlight

style

A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

Value

A glycanGrob object inheriting from grid::gTree().

Examples

grob <- glycanGrob("Gal(b1-3)GalNAc(a1-")
grid::grid.draw(grob)

Create a glycan drawing style

Description

glydraw_style() collects the rendering options shared by glydraw's standalone drawings, grobs, ggplot2 layers, guides, and glycan scales. Supply the result with ⁠style =⁠ to reuse a visual specification. Explicit rendering arguments supplied to a drawing function override the style.

Usage

glydraw_style(
  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

show_linkage

Whether to show glycosidic linkage annotations.

orient

Glycan drawing orientation: "H" for horizontal or "V" for vertical.

fuc_orient

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

red_end

Reducing-end annotation. Use "~" for a wave.

edge_linewidth

Linewidth of glycosidic linkages.

node_linewidth

Linewidth of node borders.

node_size

Multiplier for the default node size.

colors

Optional named character vector of monosaccharide fill-color overrides.

Value

A glydraw_style object.

Examples

vertical_style <- glydraw_style(orient = "V", show_linkage = FALSE)
draw_cartoon("Gal(b1-3)GalNAc(a1-", style = vertical_style)

Use glycan cartoons as legend labels

Description

guide_glycan() is a legend guide that replaces the usual text labels with glycan cartoons while retaining the legend keys drawn by the plot layers. Mapped discrete values and values returned by the scale's labels argument may be glycan structure strings supported by glyparse::auto_parse() or glyrepr::glycan_structure() vectors.

Usage

guide_glycan(
  title = ggplot2::waiver(),
  theme = NULL,
  position = NULL,
  direction = NULL,
  override.aes = list(),
  nrow = NULL,
  ncol = NULL,
  reverse = FALSE,
  order = 0,
  size = 0.4,
  orient = c("H", "V"),
  hjust = 0,
  vjust = vjust_red_end(),
  show_linkage = TRUE,
  red_end = "",
  fuc_orient = c("flex", "up"),
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  colors = NULL,
  style = NULL
)

Arguments

title

A character string or expression indicating a title of guide. If NULL, the title is not shown. By default (waiver()), the name of the scale object or the name specified in labs() is used for the title.

theme

A theme object to style the guide individually or differently from the plot's theme settings. The theme argument in the guide partially overrides, and is combined with, the plot's theme. Arguments that apply to a single legend are respected, most of which have the legend-prefix. Arguments that apply to combined legends (the legend box) are ignored, including legend.position, ⁠legend.justification.*⁠, legend.location and ⁠legend.box.*⁠.

position

A character string indicating where the legend should be placed relative to the plot panels. One of "top", "right", "bottom", "left", or "inside".

direction

A character string indicating the direction of the guide. One of "horizontal" or "vertical".

override.aes

A list specifying aesthetic parameters of legend key. See details and examples.

nrow, ncol

The desired number of rows and column of legends respectively.

reverse

logical. If TRUE the order of legends is reversed.

order

positive integer less than 99 that specifies the order of this guide among multiple guides. This controls the order in which multiple guides are displayed, not the contents of the guide itself. If 0 (default), the order is determined by a secret algorithm.

size

Positive scalar that uniformly scales each legend-label cartoon. Defaults to 0.4.

orient

Glycan drawing orientation, either "H" for horizontal or "V" for vertical. Defaults to "H".

hjust

Horizontal cartoon justification between 0 and 1, or hjust_red_end(). It defaults to 0 for horizontal cartoons and hjust_red_end() for vertical cartoons.

vjust

Vertical cartoon justification between 0 and 1, or vjust_red_end(). It defaults to vjust_red_end() for horizontal cartoons and 0.5 for vertical cartoons.

show_linkage

Whether to show glycosidic linkage annotations inside the cartoons. Defaults to TRUE.

red_end

Reducing-end annotation passed to glycanGrob(). Use "~" for a wave, or another string to display that text. Defaults to "".

fuc_orient

Fuc-like triangle orientation passed to glycanGrob().

edge_linewidth

Linkage linewidth passed to glycanGrob().

node_linewidth

Node-border linewidth passed to glycanGrob().

node_size

Node-size multiplier passed to glycanGrob().

colors

Optional named character vector of monosaccharide fill colors passed to glycanGrob().

style

A glydraw_style object that supplies rendering options. Explicitly supplied rendering arguments override it.

Value

A ggplot2 legend guide that draws glycan cartoons in place of text labels.

Examples

glycans <- data.frame(
  structure = c(
    "Gal(b1-3)GalNAc(a1-",
    "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-"
  ),
  abundance = c(12, 8)
)

ggplot2::ggplot(
  glycans,
  ggplot2::aes(
    x = .data$structure,
    y = .data$abundance,
    fill = .data$structure
  )
) +
  ggplot2::geom_col() +
  ggplot2::scale_fill_discrete(guide = guide_glycan())

Anchor glycan cartoons at their reducing ends

Description

These helpers align the reducing end of every glycan cartoon with its anchor in geom_glycan(), scale_x_glycan(), scale_y_glycan(), or guide_glycan(). Use hjust_red_end() for horizontal alignment when orient = "V", and use vjust_red_end() for vertical alignment when orient = "H". Because the required justification is calculated separately from each cartoon's rendered bounds, the helpers also work for collections of glycans with different asymmetric branches. Glycan scales and guides use reducing-end justification by default along the axis perpendicular to the drawing orientation; geom_glycan() remains centered by default.

Usage

hjust_red_end()

vjust_red_end()

Value

A reducing-end justification marker accepted by the glycan layer, scales, and guide.

Examples

glycan <- data.frame(
  x = 0,
  y = 0,
  structure = "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-"
)

ggplot2::ggplot(
  glycan,
  ggplot2::aes(x = .data$x, y = .data$y, structure = .data$structure)
) +
  geom_glycan(orient = "V", hjust = hjust_red_end())

ggplot2::ggplot(
  glycan,
  ggplot2::aes(x = .data$x, y = .data$y, structure = .data$structure)
) +
  geom_glycan(orient = "H", vjust = vjust_red_end())

Print glycan cartoon

Description

Print glycan cartoon

Usage

## S3 method for class 'glydraw_cartoon'
print(x, ..., newpage = is.null(vp), vp = NULL)

Arguments

x

A ggplot2 object returned by draw_cartoon().

...

Ignored.

newpage

Draw the plot on a new page.

vp

A grid viewport object or viewport name.

Value

The original glycan cartoon, invisibly.

Save fixed-size glycan cartoon image to local device.

Description

This function saves the glycan cartoon to a file, with a suitable size.

Usage

save_cartoon(cartoon, file, ..., dpi = 300, scale = 1)

Arguments

cartoon

A ggplot2 object returned by draw_cartoon().

file

File name of glycan cartoon.

...

Ignored.

dpi

Deprecated and ignored. Use scale to change the output size.

scale

Numeric output-size multiplier. The default 1 saves the cartoon at its natural fixed size; 2 saves the same cartoon with twice the pixel width and height.

Value

Path of the saved cartoon file.

Why not `width` and `height`?

Examples

cartoon <- draw_cartoon("Gal(b1-3)GalNAc(a1-")
save_cartoon(cartoon, tempfile(fileext = ".png"))

Use glycan cartoons as axis labels

Description

scale_x_glycan() and scale_y_glycan() are discrete position scales that replace text tick labels with compact glycan cartoons. Mapped discrete values and values returned by the scale's labels argument may be glycan structure strings supported by glyparse::auto_parse() or glyrepr::glycan_structure() vectors. X-axis cartoons are vertical and bottom-aligned by default, while y-axis cartoons are horizontal and right-aligned by default. The cartoon orientation and alignment adapt to the displayed axis, including when the axes are swapped by ggplot2::coord_flip().

Usage

scale_x_glycan(
  name = ggplot2::waiver(),
  ...,
  palette = seq_len,
  expand = ggplot2::waiver(),
  position = "bottom",
  sec.axis = ggplot2::waiver(),
  continuous.limits = NULL,
  size = 0.4,
  angle = 0,
  hjust = hjust_red_end(),
  vjust = 0,
  nudge_x = 0,
  nudge_y = 0,
  show_linkage = TRUE,
  red_end = "",
  fuc_orient = c("flex", "up"),
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  colors = NULL,
  style = NULL
)

scale_y_glycan(
  name = ggplot2::waiver(),
  ...,
  palette = seq_len,
  expand = ggplot2::waiver(),
  position = "left",
  sec.axis = ggplot2::waiver(),
  continuous.limits = NULL,
  size = 0.4,
  angle = 0,
  hjust = 1,
  vjust = vjust_red_end(),
  nudge_x = 0,
  nudge_y = 0,
  show_linkage = TRUE,
  red_end = "",
  fuc_orient = c("flex", "up"),
  edge_linewidth = 0.8,
  node_linewidth = 0.8,
  node_size = 1,
  colors = NULL,
  style = NULL
)

Arguments

name

The name of the scale, displayed as the axis title. Use NULL to remove the title.

...

Arguments passed to ggplot2::scale_x_discrete() or ggplot2::scale_y_discrete(), including breaks and labels.

palette

A palette function that returns discrete position values.

expand

Expansion applied to the discrete position scale.

position

Position of the axis.

sec.axis

A secondary axis specification.

continuous.limits

Continuous limits used to position the discrete scale.

size

Positive scalar that uniformly scales each axis-label cartoon. Defaults to 0.4.

angle

Rotation in degrees applied to each axis-label cartoon, independently of the cartoon orientation. Defaults to 0.

hjust

Horizontal justification. Vertical x-axis cartoons default to hjust_red_end(), while horizontal y-axis cartoons default to 1.

vjust

Vertical justification. Vertical x-axis cartoons default to 0, while horizontal y-axis cartoons default to vjust_red_end().

nudge_x

Horizontal adjustment of each cartoon, in millimetres. Positive values move cartoons to the right. When this moves cartoons toward or away from a y-axis title, the title moves with them to preserve the gap. Defaults to 0.

nudge_y

Vertical adjustment of each cartoon, in millimetres. Positive values move cartoons upward. When this moves cartoons toward or away from an x-axis title, the title moves with them to preserve the gap. Defaults to 0.

show_linkage

Whether to show glycosidic linkage annotations inside the cartoons. Defaults to TRUE.

red_end

Reducing-end annotation passed to glycanGrob(). Use "~" for a wave, or another string to display that text. Defaults to "".

fuc_orient

Fuc-like triangle orientation passed to glycanGrob().

edge_linewidth

Linkage linewidth passed to glycanGrob().

node_linewidth

Node-border linewidth passed to glycanGrob().

node_size

Node-size multiplier passed to glycanGrob().

colors

Optional named character vector of monosaccharide fill colors passed to glycanGrob().

style

A glydraw_style object that supplies rendering options. Its orientation is ignored because each scale determines the axis direction. Explicitly supplied rendering arguments override it.

Value

A ggplot2 discrete position scale.

Examples

glycans <- data.frame(
  structure = c(
    "Gal(b1-3)GalNAc(a1-",
    "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-"
  ),
  abundance = c(12, 8)
)

ggplot2::ggplot(glycans, ggplot2::aes(x = structure, y = abundance)) +
  ggplot2::geom_col() +
  scale_x_glycan()

Package {glydraw}

glydraw: Draw Beautiful Symbol Nomenclature for Glycans

Description

Author(s)

See Also

Draw a Symbol Nomenclature For Glycan (SNFG)

Description

Usage

Arguments

Value

Examples

Export all glycan structures to figures

Description

Usage

Arguments

Value

File names

Why not width and height?

Examples

Draw glycans at ggplot2 positions

Description

Usage

Arguments

Value

Aesthetics

Examples

Draw glycans as ggraph nodes

Description

Usage

Arguments

Value

Aesthetics

Examples

Construct a glycan grob

Description

Usage

Arguments

Value

Examples

Create a glycan drawing style

Description

Usage

Arguments

Value

Examples

Use glycan cartoons as legend labels

Description

Usage

Arguments

Value

Examples

Anchor glycan cartoons at their reducing ends

Description

Usage

Value

Examples

Print glycan cartoon

Description

Usage

Arguments

Value

Save fixed-size glycan cartoon image to local device.

Description

Usage

Arguments

Value

Why not width and height?

Examples

Use glycan cartoons as axis labels

Description

Usage

Arguments

Value

Examples

Why not `width` and `height`?

Why not `width` and `height`?