Plot a permutation difference network e experiment object

Usage

plot_perm_diff_network(
  e,
  permutation_group,
  channel = "cfos",
  layout = "stress",
  seed = 30,
  degree_scale_limit = c(1, 15),
  node_size_range = c(3, 15),
  edge_color_pos = "#04C3C3",
  edge_color_neg = "#BF1F1F",
  anatomical.colors = c(Isocortex = "#70ff71", OLF = "#75aadb", HPF = "#7ed04b", CTXsp =
    "#8ada87", CNU = "#98d6f9", TH = "#ff7080", HY = "#e64438", MB = "#ff64ff", HB =
    "#ff9b88"),
  pos_edge_legend_label = "",
  neg_edge_legend_label = "",
  correlation_edge_width_limit = c(0, 2),
  edge_thickness_range = c(0, 6),
  node_text_size = 12,
  graph_theme = NULL,
  mark_hull = TRUE,
  save_plot = TRUE,
  height = 15,
  width = 15,
  image_ext = ".png"
)

Arguments

e: experiment object
permutation_group: (str) Supply names of the specific analyses found under e$permutation_p_matrix %>% names()
channel: (str, default = "cfos")
layout: (str, default = "stress") equivalent to the ggraph layout parameter.
seed: random seed for replication
degree_scale_limit: (vec, default = c(1,15)) Scale limit for degree size
node_size_range: (default = c(1,8)) Node size range.
edge_color_pos: (str, default = "#04C3C3") Color of the edges representing positive correlation differences
edge_color_neg: (str, default = "#BF1F1F") Color of the edges representing negative correlation differences
anatomical.colors: (vec, default = c(Isocortex = "#70ff71", OLF = "#75aadb", HPF = "#7ed04b", CTXsp = "#8ada87", CNU = "#98d6f9", TH = "#ff7080", HY = "#e64438", MB = "#ff64ff", HB = "#ff9b88")) Colors for the parent region as a named vector of hexadecimal regions.
pos_edge_legend_label: (str, default = "") Legend label for positive difference edges, e.g. "Iso > Ctrl"
neg_edge_legend_label: (str, default = "") Legend label for negative difference edges, e.g. "Iso < Ctrl"
correlation_edge_width_limit: (default = c(0, 2)) Range of correlation differences in the network.
edge_thickness_range: (default = c(0,6)) Range for the width size of the edges.
node_text_size: (default = 12) Font size for node text.
graph_theme: (default = NULL) Add a ggraph::theme_graph() to the network graph. If NULL, the default is taken.
mark_hull: (bool, default = TRUE) Plot detected communities using a convex hull polygon.
save_plot: (bool, default = TRUE) Save into the figures subdirectory of the the experiment object output folder.
height: Height of the plot in inches.
width: width of the plot in inches.
image_ext: (default = ".png")

Value

p A plot handle.

Examples

if (FALSE) {
p <- plot_perm_diff_network(anesthesia,
permutation_group = "Control_vs_Isoflurane",
channel = "cfos",
pos_edge_legend_label = "Iso > Ctrl",
neg_edge_legend_label = "Iso < Ctrl",
layout = "fr",
mark_hull=TRUE,
node_text_size = 14,
seed = 15,
width = 20,
height = 20,
graph_theme = graph_theme,
anatomical.colors = anatomical.colors,
image_ext = ".png")
}