plot_dynamic_networks: Plot dynamic networks

In inferCSN: Inferring Cell-Specific Gene Regulatory Network

Plot dynamic networks

Description

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, ]
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"
)

## Not run: 
# 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"
)

## End(Not run)

inferCSN documentation built on Sept. 11, 2024, 9:32 p.m.