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Title:

Plot Glycans using 'ggplot2'

Version:

0.0.3

Description:

Plot glycans following the Symbol Nomenclature for Glycans (SNFG) using 'ggplot2'. SNFG provides a standardized visual representation of glycan structures.

License:

Artistic-2.0

Encoding:

UTF-8

Depends:

R (≥ 4.1.0)

Imports:

dplyr, ggplot2, ggtangle (≥ 0.1.0), ggstar, ggrepel, igraph, rlang, yulab.utils

Suggests:

quarto

VignetteBuilder:

quarto

RoxygenNote:

7.3.3

NeedsCompilation:

Packaged:

2026-01-13 05:19:09 UTC; HUAWEI

Author:

Guangchuang Yu

[aut, cre]

Maintainer:

Guangchuang Yu <guangchuangyu@gmail.com>

Repository:

CRAN

Date/Publication:

2026-01-18 11:00:08 UTC

Format Linkage Labels

Description

Converts 'a'/'b' to Greek letters alpha/beta.

Usage

format_linkage_label(labels)

Arguments

labels

A character vector of linkage labels.

Value

A character vector with Greek letters.

Examples

labels <- c("a1-3", "b1-4")
format_linkage_label(labels)

Glycan Geometry Layer

Description

A convenient wrapper to add edges, edge labels, and SNFG nodes to a glycan plot.

Usage

geom_glycan(
  edge_color = "black",
  edge_width = 0.5,
  arrow_length = unit(2, "mm"),
  node_size = 5,
  node_label = FALSE,
  label_size = 3.88,
  edge_label_size = 3.88,
  ...
)

Arguments

edge_color

Color of the edges.

edge_width

Width of the edges.

arrow_length

Length of the edge arrows.

node_size

Size of the node symbols.

node_label

Logical. Whether to show node labels (monosaccharide names). Default is FALSE.

label_size

Size of the node labels.

edge_label_size

Size of the edge labels (linkage).

...

Additional arguments (currently unused).

Value

A list of 'ggplot2' layers.

Examples

s <- "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc"
## Not run: 
gglycan(s) + geom_glycan()

## End(Not run)

Get Highlight Alpha

Description

Gets the current alpha value for motif highlighting.

Usage

get_hl_alpha(default = 0.4)

Arguments

default

Default value if not set (0.4).

Value

A numeric value representing the alpha level.

Examples

get_hl_alpha()

Plot Glycan Structure

Description

Visualizes a glycan structure using ggplot2 and ggtangle.

Usage

gglycan(
  data,
  mapping = aes(),
  layout = ggtangle::layout_fishbone,
  direction = "left",
  length = 1,
  angle_sep = 30,
  motif = NULL,
  ...
)

Arguments

data

A glycan graph object (from 'read_glycan') or an IUPAC string.

mapping

Default list of aesthetic mappings to use for plot.

layout

The layout algorithm to use. Default is 'ggtangle::layout_fishbone'. Can be a string ("tree", "nicely") or a function.

direction

The direction of the main chain growth ("left", "right", "up", "down"). Default is "left".

length

The distance between nodes. Default is 1.

angle_sep

The angle separation for branches in degrees. Default is 30.

motif

A motif string (IUPAC format) to highlight in the structure. Default is NULL.

...

Additional arguments passed to 'ggplot'.

Value

A 'ggplot' object.

Examples

s <- "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc"
## Not run: 
gglycan(s) + geom_glycan()

## End(Not run)

Identify Motif in Glycan Graph

Description

Finds occurrences of a motif subsequence in the main glycan graph and marks them.

Usage

highlight_motif(graph, motif_str)

Arguments

graph

The main glycan graph (an 'igraph' object).

motif_str

The motif string (IUPAC format).

Value

An 'igraph' object with an added 'alpha' vertex attribute (1 for motif, 0.4 for others).

Examples

s <- "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc"
g <- read_glycan(s)
g <- highlight_motif(g, "Neu5Ac(a2-3)Gal(b1-4)GlcNAc")

Match SNFG Style to Graph Nodes

Description

Maps glycan node labels to SNFG shapes and colors.

Usage

match_snfg_style(graph)

Arguments

graph

An 'igraph' object.

Value

An 'igraph' object with additional vertex attributes: 'snfg_shape' (numeric starshape) and 'snfg_fill' (color).

Examples

s <- "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc"
g <- read_glycan(s)
g <- match_snfg_style(g)

Read Glycan Data

Description

Parses a glycan string (IUPAC condensed format) and returns a graph object.

Usage

read_glycan(x, format = "iupac")

Arguments

x

A character string representing the glycan structure.

format

The format of the string. Currently only "iupac" is supported.

Value

An 'igraph' object representing the glycan structure.

Examples

s <- "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc"
g <- read_glycan(s)

Set Highlight Alpha

Description

Sets the alpha value for motif highlighting.

Usage

set_hl_alpha(value = 0.4)

Arguments

value

Numeric value for alpha (default 0.4).

Value

No return value, called for side effects.

Examples

set_hl_alpha(0.5)

SNFG Symbol Mapping

Description

A dataset containing the shapes and colors for SNFG symbols.

Usage

snfg_map

Format

A data frame with columns:

monosaccharide: The name of the monosaccharide (e.g., Glc, Gal, Man)
shape: The shape of the symbol (e.g., circle, square)
color: The fill color of the symbol (hex code)
starshape: The ggstar shape ID