Plot network as directed graph
plot.network.RdThis function plots a network object as a directed graph using ggplot2. Nodes represent neurons, and directed edges represent connections between them. The plot can be customized by selecting which motif to display and how to color the edges.
Usage
# S3 method for class 'network'
plot(
network,
title = NULL,
plot_motif = "local connections",
edge_color = "pre_type",
cell_color = "layer",
cell_size_factor = 5,
arrow_size_factor = 0.5,
return_plot = FALSE
)Arguments
- network
Network object to plot.
- title
Title for the plot (default: "Cortical Patch" or network name (if provided), plus plot motif name(s)).
- plot_motif
Character string specifying which motif to plot; options include "local" for local connections within each node or the name of a long-range projection motif (default: "local connections").
- edge_color
Character string specifying how to color the edges; options include "pre_type" to color by presynaptic neuron type, "post_type" to color by postsynaptic neuron type, or "motif" to color by motif type (default: "pre_type").
- cell_color
Character string specifying how to color the nodes; options include "layer" to color by layer index or "type" to color by neuron type (default: "layer").
- cell_size_factor
Numeric value controlling how cell size in the plot scales to the number of cells.
- return_plot
Logical indicating whether to return the ggplot object (TRUE) or print the plot directly (FALSE) (default: FALSE).
- arrow_size
Numeric value indicating the size of the arrows representing edges (default: 0.05).