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glydraw

Lifecycle: experimental CRAN status R-universe version R-CMD-check Codecov test coverage

glydraw is a ggplot2-native R engine for drawing reproducible SNFG glycan cartoons from glycan structure objects or text notations, with support for batch export, structural highlighting, and deep appearance customization.

Installation

Install glycoverse

We recommend installing the meta-package glycoverse, which includes this package and other core glycoverse packages.

Install glydraw alone

If you don’t want to install all glycoverse packages, you can only install glydraw.

You can install the latest release of glydraw from CRAN:

install.packages("glydraw")

Or from r-universe:

install.packages('glydraw', repos = c('https://glycoverse.r-universe.dev', 'https://cloud.r-project.org'))

Or from GitHub:

remotes::install_github("glycoverse/glydraw@*release")

Or install the development version:

remotes::install_github("glycoverse/glydraw")

Example

Plot one glycan

library(glydraw)

glycan <- paste0(
  "Glc(a1-2)Glc(a1-3)Glc(a1-3)Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-3)",
  "[Man(a1-2)Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(a1-"
)
draw_cartoon(glycan, red_end = "PP-Dol")

ggplot2 extension

scale_x_glycan() and scale_y_glycan() can add glycan cartoons to standard ggplot2 figures. For example, you can use glycan cartoons as labels in a heatmap:

library(ggplot2)
library(glydraw)
library(tibble)

set.seed(123)
plot_data <- tibble(
  `z-score` = rnorm(25),
  branch = rep(c(
    "GlcNAc(??-",
    "Gal(??-?)GlcNAc(??-",
    "Neu5Ac(??-?)Gal(??-?)GlcNAc(??-",
    "Neu5Ac(??-?)Gal(??-?)[Fuc(??-?)]GlcNAc(??-",
    "Gal(??-?)[Fuc(??-?)]GlcNAc(??-"
  ), 5),
  sample = rep(paste0("Sample ", 1:5), each = 5)
)

ggplot(plot_data, aes(branch, sample)) +
  geom_tile(aes(fill = `z-score`), color = "white", linewidth = 1) +
  scale_fill_viridis_c(option = "plasma") +
  scale_x_glycan(
    position = "top",
    size = 0.2,
    show_linkage = FALSE,
    red_end = "~"
  ) +
  coord_equal() +
  theme_void() +
  theme(axis.text.y = element_text())

glycan <- paste0(
  "Neu5Ac(a2-3)Gal(b1-3)[Fuc(a1-2)Gal(b1-3)[Fuc(a1-4)]GlcNAc(b1-3)",
  "[Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-6)]Gal(b1-4)GlcNAc(b1-6)]GalNAc(a1-"
)
draw_cartoon(glycan, red_end = "~", node_size = 1.2)

glycan <- "Gal(b1-3)[Neu5Ac(a2-3)Gal6S(b1-4)[Fuc(a1-3)]GlcNAc(b1-6)]GalNAc(a1-"
draw_cartoon(glycan, orient = "V", red_end = "Ser/Thr")

glycan <- "Fuc(a1-3)[Fuc(a1-6)]GlcNAc(b1-"
draw_cartoon(glycan, orient = "V", red_end = "Asn", fuc_orient = "up")

glycan <- paste0(
  "WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*N][a1122h-1a_1-5_2*OP^XOCCN/3O/3=O]",
  "[a1122h-1a_1-5_6*OP^XOCCN/3O/3=O]/1-2-3-3/a4-b1_b6-c1_c2-d1"
)
draw_cartoon(glycan)

glycan <- "Glc(b1-4)[Xyl(a1-6)][Xyl(a1-2)]Glc(b1-4)[Xyl(a1-6)]Glc(b1-4)[Fuc(a1-2)Gal(b1-2)Xyl(a1-6)]Glc(b1-4)Glc(b1-4)[Xyl(a1-6)]Glc(b1-"
draw_cartoon(glycan, fuc_orient = "up")

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