Plot network graph.

Plot network graph.

plot_network_graph(object, ...)

# S4 method for class 'CSNObject'
plot_network_graph(
  object,
  network = DefaultNetwork(object),
  celltypes = NULL,
  graph = "module_graph",
  layout = "umap",
  edge_width = 0.2,
  edge_color = c(`-1` = "darkgrey", `1` = "orange"),
  node_color = pals::magma(100),
  node_size = c(1, 5),
  text_size = 10,
  color_nodes = TRUE,
  label_nodes = TRUE,
  color_edges = TRUE,
  ...
)

Arguments

object

The input data, a csn object.

...

Arguments for other methods

network

Name of the network to use.

celltypes

Celltypes to plot. If NULL, all celltypes are plotted.

graph

Name of the graph.

layout

Layout for the graph. Can be 'umap' or any force-directed layout implemented in ggraph

edge_width

Edge width.

edge_color

Edge color.

node_color

Node color or color gradient.

node_size

Node size range.

text_size

Font size for labels.

color_nodes

Logical, Whether to color nodes by centrality.

label_nodes

Logical, Whether to label nodes with gene name.

color_edges

Logical, Whether to color edges by direction.

Value

A CSNObject object.