inferCSN (version 1.2.0)

plot_dynamic_networks: 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
)

Value

A dynamic figure object.

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.

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"
)

if (FALSE) {
# 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"
)
}