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.
title: The title of figure.
theme_type: Default is theme_void, the theme of figure, could be theme_void, theme_blank or theme_facet.
plot_type: Default is "ggplot", the type of figure, could be ggplot, animate or ggplotly.
layout: Default is "fruchtermanreingold", the layout of figure, could be fruchtermanreingold or kamadakawai.
nrow: The number of rows of figure.
figure_save: Default is FALSE, Logical value, whether to save the figure file.
figure_name: The name of figure file.
figure_width: The width of figure.
figure_height: The height of figure.
seed: Default is 1, the seed random use to plot network.

Value

A dynamic figure object

Examples

data("example_matrix")
network <- inferCSN(example_matrix)[1:100, ]
#> ℹ [2025-05-07 09:38:42] Running for <dense matrix>.
#> ℹ [2025-05-07 09:38:42] Checking input parameters.
#> ℹ [2025-05-07 09:38:42] Using L0 sparse regression model.
#> ℹ [2025-05-07 09:38:42] Using 1 core
#> ✔ [2025-05-07 09:38:42] 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
)


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"
)
} # }