Plot dynamic networks

Usage

plot_dynamic_networks(
  network_table,
  celltypes_order,
  ntop = 10,
  title = NULL,
  theme_type = "theme_void",
  plot_type = "ggplot",
  layout = "fruchtermanreingold",
  nrow = 2,
  figure_save = FALSE,
  figure_name = NULL,
  figure_width = 6,
  figure_height = 6,
  seed = 1
)

Arguments

network_table: The weight data table of network.
celltypes_order: The order of cell types.
ntop: The number of top genes to plot. Default is 10.
title: The title of figure. Default is NULL.
theme_type: The theme of figure. Could be "theme_void", "theme_blank", or "theme_facet". Default is "theme_void".
plot_type: The type of figure. Could be "ggplot", "animate", or "ggplotly". Default is "ggplot".
layout: The layout of figure. Could be "fruchtermanreingold" or "kamadakawai". Default is "fruchtermanreingold".
nrow: The number of rows of figure. Default is 2.
figure_save: Whether to save the figure file. Default is FALSE.
figure_name: The name of figure file. Default is NULL.
figure_width: The width of figure. Default is 6.
figure_height: The height of figure. Default is 6.
seed: The seed random use to plot network. Default is 1.

Value

A dynamic figure object.

Examples

data(example_matrix)
network <- inferCSN(example_matrix)[1:100, ]
#> ℹ [2025-10-16 02:36:48] Running for <dense matrix>.
#> ◌ [2025-10-16 02:36:48] Checking input parameters...
#> ℹ [2025-10-16 02:36:48] Using `L0` sparse regression model
#> ℹ [2025-10-16 02:36:48] Using 1 core
#> ℹ [2025-10-16 02:36:48] Building results
#> ✔ [2025-10-16 02:36:48] Run done.
network$celltype <- c(
  rep("cluster1", 20),
  rep("cluster2", 20),
  rep("cluster3", 20),
  rep("cluster5", 20),
  rep("cluster6", 20)
)

celltypes_order <- c(
  "cluster5", "cluster3",
  "cluster2", "cluster1",
  "cluster6"
)

plot_dynamic_networks(
  network,
  celltypes_order = celltypes_order
)
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the inferCSN package.
#>   Please report the issue at <https://github.com/mengxu98/inferCSN/issues>.


plot_dynamic_networks(
  network,
  celltypes_order = celltypes_order[1:3]
)


plot_dynamic_networks(
  network,
  celltypes_order = celltypes_order,
  plot_type = "ggplotly"
)


if (FALSE) { # \dontrun{
# If setting `plot_type = "animate"` to plot and save `gif` figure,
# please install `gifski` package first.
plot_dynamic_networks(
  network,
  celltypes_order = celltypes_order,
  plot_type = "animate"
)
} # }