Plot the mean degree of the networks in a barplot. Error bars are plotted as SEM.

Usage

plot_mean_degree(
  e,
  color_palettes = c("reds", "greens"),
  colors_manual = NULL,
  channels = c("cfos", "eyfp"),
  labels = c(AD = "AD_label", control = "control_label"),
  title = "my_title",
  height = 10,
  width = 10,
  label_angle = 60,
  rev_x_scale = FALSE,
  ylim = c(0, 70),
  image_ext = ".png",
  print_plot = TRUE,
  save_plot = TRUE
)

Arguments

e: experiment object
color_palettes: (str, default = c("reds", "greens")) Color palettes from grDevices::hcl.colors that are used to for plotting networks for each channel, respectively.
colors_manual: (str, default = NULL ) Manually choose the hexadecimal color codes to create a custom color palette, e.g. colors_manual = c("#660000", "#FF0000", "#FF6666"). Warning: this will be applied to all channels. It's recommended to set the channels parameter to a single channel if this parameter is used.
channels: (str, default = c("cfos", "eyfp", "colabel")) Channels to plot
labels: (str) The legend labels to correspond with your network names, e.g. labels = c(network1_name = "network 1 label", network2_name = "network 2 label). These are the same network names used in the function summarise_networks().
title: (str, default = "my_title) plot title
height: (int, default = 10) Height of the plot in inches.
width: (int, default = 10) Width of the plot in inches.
label_angle: (int, default = 60)
rev_x_scale: (bool, default = FALSE) Reveres the scale of the categorical variables the experiment object output folder.
ylim: (vec, default = c(0,10)) Axes limits of y-axis
image_ext: (default = ".png") image extension to the plot as.
print_plot: (bool, default = TRUE) Whether to print the plot as an output.s
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.