View motif matches on a glycan

Visualize where a motif matches a glycan structure.

Usage

view_motif(
  glycan,
  motif,
  alignment = NULL,
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL
)

Arguments

glycan

One of:

• A scalar glyrepr::glycan_structure().

• A glycan structure string. All formats supported by glyparse::auto_parse() are accepted, including IUPAC-condensed, WURCS, GlycoCT, and others.

motif

One of:

• A glyrepr::glycan_structure() scalar.

• A glycan structure string, supported by glyparse::auto_parse().

• A known motif name (use db_motifs() to see all available motifs).

alignment

A character string. Possible values are "substructure", "core", "terminal", and "whole". If not provided, the value will be decided based on the motif argument. If motif is a motif name, the alignment in the database will be used. Otherwise, "substructure" will be used.

ignore_linkages

A logical value. If TRUE, linkages will be ignored in the comparison. Default is FALSE.

strict_sub

A logical value. If TRUE (default), substituents will be matched in strict mode, which means if the glycan has a substituent in some residue, the motif must have the same substituent to be matched.

match_degree

A logical vector indicating which motif nodes must match the glycan's in- and out-degree exactly. For have_motif(), count_motif(), and match_motif(), this must be a logical vector with length 1 or the number of motif nodes (length 1 is recycled). For have_motifs(), count_motifs(), and match_motifs(), this must be a list of logical vectors with length equal to motifs; each element follows the same length rules. When match_degree is provided, alignment and alignments are silently ignored.

Value

A ggplot object returned by glydraw::draw_cartoon(). If no match is found, the glycan is drawn without highlighted residues and a cli alert is emitted.

Details

view_motif() matches one motif against one glycan with the same matching rules used by match_motif(), then draws the glycan with the matched residues highlighted.

See also

match_motif(), glydraw::draw_cartoon()

Examples

library(glyparse)
library(glyrepr)

glycan <- n_glycan_core()
motif <- parse_iupac_condensed("Man(a1-3)[Man(a1-6)]Man(b1-")

if (FALSE) { # \dontrun{
view_motif(glycan, motif)
} # }