Skip to contents

Plot the results of the permutation histogram used to determine the p-value of the pairwise region comparison

volcano_plot.Rd

Create a Volcano plot.

Usage

volcano_plot(
  e,
  permutation_comparison = "female_AD_vs_male_AD",
  channels = c("cfos", "eyfp", "colabel"),
  colors = c("#be0000", "#00782e", "#f09b08"),
  save_plot = TRUE,
  title = NULL,
  ylim = c(0, 3),
  height = 8,
  width = 10,
  print_plot = TRUE,
  plt_theme = NULL,
  point_size = 1,
  image_ext = ".png"
)

Arguments

e

experiment object

permutation_comparison

The name of the correlation group comparisons to plot.

channels

(str, default = c("cfos", "eyfp", "colabel")) channels to plot.

colors

(str, default = c("#be0000", "#00782e", "#f09b08")) Hexadecimal code for the colors corresponding to the channels attribute of the correlation_list. Color values can also be input compatible with ggplot2 plotting functions.

save_plot

(bool, default = TRUE) Save into the figures subdirectory of the the experiment object output folder.

title

Title of the plot.

height

height of the plot in inches.

width

width of the plot in inches.

print_plot

(bool, default = TRUE) Print the plot as graphics windows.

plt_theme

(default = NULL) Add a ggplot2::theme() to the plot. If NULL, the default is taken..

point_size

(default = 1) Size of the plotted points.

image_ext

(default = ".png") image extension to save the plot as.

Value

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

Details

Plot the correlation difference between two comparison groups into a volcano plot. The function correlation_diff_permutation() must be run first in order to generate results to plot.

Examples

volcano_plot(e, permutation_comparison = "female_AD_vs_male_AD", channels = c("cfos", "eyfp", "colabel"),
colors =  c("#be0000", "#00782e", "#f09b08"), save_plot = TRUE, title = NULL, ylim = c(0, 3), height = 8,
width = 10, print_plot = TRUE, image_ext = ".png")
#> Error in volcano_plot(e, permutation_comparison = "female_AD_vs_male_AD",     channels = c("cfos", "eyfp", "colabel"), colors = c("#be0000",         "#00782e", "#f09b08"), save_plot = TRUE, title = NULL,     ylim = c(0, 3), height = 8, width = 10, print_plot = TRUE,     image_ext = ".png"): object 'e' not found