Package 'gglycan'

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

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