Plot the networks stored in an experiment object

Usage

plot_networks(
  e,
  network_name = "AD",
  title = NULL,
  channels = c("cfos", "eyfp", "colabel"),
  edge_color = "firebrick",
  height = 15,
  width = 15,
  edge_type = "arc",
  region_legend = TRUE,
  degree_scale_limit = c(1, 10),
  anatomical.colors = NULL,
  correlation_edge_width_limit = c(0.8, 1),
  image_ext = ".png",
  print_plot = FALSE,
  graph_theme = NULL,
  label_size = 5,
  edge_thickness_range = c(1, 5),
  node_size_range = c(1, 8),
  label_offset = 0.15,
  save_plot = TRUE
)

Arguments

e: experiment object
network_name: (str, default = "AD")
title: (str, default = NULL) Title of network plot
channels: (str, default = c("cfos", "eyfp", "colabel"))
edge_color: (str, default = "firebrick") Color of the network edges.
height: Height of the plot in inches.
width: width of the plot in inches.
edge_type: (default = "arc") "arc" or "diagonal".
region_legend: (default = TRUE) Boolean determining whether or not to show the region legend categorizing subregions into their largest parent region. Only works well if the Allen ontology is used for the dataset.
degree_scale_limit: (vec, default = c(1,10)) Scale limit for degree size
anatomical.colors: (vector, default = NULL) NULL defaults to viridis. A named vector of hexadecimal codes for the anatomical super regions. e.g. anatomical.colors = c(Isocortex = "#5571a9", OLF = "#64bdc4", HPF = "#d2875b", CTXsp = "#87a3db", CNU = "#466496", TH = "#7e72af", HY = "#8e7960", MB = "#d796c8", HB = "#646464")
correlation_edge_width_limit: (default = c(0.8,1))
image_ext: (default = ".png") image extension to the plot as.
print_plot: (bool, default = FALSE) Whether to print the plot as an output. the experiment object output folder.
graph_theme: (default = NULL) Add a ggraph::theme_graph() to the network graph. If NULL, the default is taken.
label_size: (default = 5) Default font size for network region labels.
edge_thickness_range: (default = c(1,5)) Thickness range of the edges.
node_size_range: (default = c(1,8)) Node size range. Can also be a hexadecimal color code written as a string.
label_offset: (default = 0.15) Distance of label from nodes.
save_plot: (bool, default = TRUE) Save into the figures subdirectory of the the experiment object output folder.

Value

p_list A list the same length as the number of channels, with each element containing a plot handle for that channel.

Examples

if (FALSE) {
p <- plot_networks(e, network_name = "Shock", channels = "cfos")
}