Plot the networks stored in an experiment object

Usage

plot_joined_networks(
  e,
  correlation_list_names = c("male_agg", "female_non"),
  title = NULL,
  channels = "cfos",
  absolute_weight = TRUE,
  edge_colors = c(male_agg_pos = "#06537f", male_agg_neg = "#526c7a", female_non_pos =
    "#C70039", female_non_neg = "#71585f"),
  edge_color_labels = c(male_agg_pos = "Positive male", male_agg_neg = "Negative male",
    female_non_pos = "Positive female", female_non_neg = "Negative female"),
  height = 15,
  width = 15,
  region_legend = TRUE,
  degree_scale_limit = c(1, 10),
  correlation_edge_width_limit = c(0.8, 1),
  image_ext = ".png",
  print_plot = FALSE,
  graph_theme = NULL,
  transparent_edge_group1 = TRUE,
  transparent_edge_group2 = FALSE,
  label_size = 5,
  label_offset = 0.15,
  edge_thickness_range = c(1, 5),
  node_size_range = c(1, 8),
  anatomical.colors = NULL,
  save_plot = TRUE
)

Arguments

e: experiment object
correlation_list_names: (str vec) character vector of the two correlation lists used to include in a joined network, e.g., correlation_list_names = c("male_agg", "female_non")
title: (str, default = NULL) Title of network plot
channels: (str, default = c("cfos", "eyfp", "colabel"))
absolute_weight: (bool, default = TRUE) Whether to plot absolute weights. If TRUE, the edge_colors and edge_colors_label should not contain values for positive and negative correlations.
edge_colors: (vec) vector of hexidecimal codes as strings. Assign a group name to the vector element. e.g. c(male_agg_pos = "#06537f", male_agg_neg = "#526c7a", female_non_pos = "#C70039", female_non_neg = "#71585f")
edge_color_labels: (vec) vector of edge labels as strings. e.g. c(male_agg_pos = "Positive male", male_agg_neg = "Negative male", female_non_pos = "Positive female", female_non_neg = "Negative female")
height: Height of the plot in inches.
width: width of the plot in inches.
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
correlation_edge_width_limit: (default = c(0.8, 1)) Range for the width size of the edges.
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.
transparent_edge_group1: (bool) logical to render edges transparent
transparent_edge_group2: (bool) logical to render edges transparent
label_size: (default = 5) Default font size for network region labels.
label_offset: (default = 0.15) Distance of label from nodes.
edge_thickness_range: (default = c(1,5))
node_size_range: (default = c(1, 8))
anatomical.colors: (NuLL or vec, default = NULL) Colors for the parent region as a named vector of hexadecimal regions. Can also be a hexadecimal color code written as a string.
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_list <- plot_joined_networks(anesthesia, correlation_list_names = c("male_agg", "female_non"),
channels = "cfos", edge_colors = c(male_agg =  "#06537f", female_non = "#C70039"),
edge_color_labels = c(male_agg = "Male aggressor", female_non = "Female non-aggressor"),
degree_scale_limit = c(1,45), correlation_edge_width_limit = c(0.8, 1.0),
height = 30, width = 30, label_size = 13, label_offset = 0.08, image_ext = ".png")
}