volcano: Generate Volcano Plot

Description

This function generates a volcano plot for differential expression analysis results.

Usage

volcano(
  data,
  x.scale,
  y.scale,
  interact = FALSE,
  FC.threshold = 2,
  P.threshold = 0.05,
  change.label = c("Up", "Down", "Notsig"),
  point.size = 2,
  point.color = c("lightsalmon2", "cadetblue", "grey"),
  x_scale_mannual = FALSE,
  y_scale_mannual = FALSE,
  linetype = 4,
  line.alpha = 0.4,
  line.color = "grey34",
  line.size = 1,
  annotation.label = NULL,
  annotation.color = "#C82423",
  text.size = 2.5,
  max.overlap = 40,
  title = NULL
)

Value

A list containing the plot object, data frame with plotted points, and omitted data points. If interact = TRUE, the html object of the interactive plot will be also returned.

Arguments

data: The data frame containing the results of differential expression analysis.
x.scale: The manual limits for the x-axis (default is NULL).
y.scale: The manual limits for the y-axis (default is NULL).
interact: Logical value indicating whteher to generate interactive volcano plot.
FC.threshold: The fold change threshold for determining significant changes (default is 2).
P.threshold: The significance threshold for p-values (default is 0.05).
change.label: The labels for differentially expressed genes (default is c('Up', 'Down', 'Notsig')).
point.size: The size of data points in the plot (default is 2).
point.color: The colors for differentially expressed genes (default is c('lightsalmon2', 'cadetblue', 'grey')).
x_scale_mannual: Logical value indicating whether to manually specify x-axis limits (default is FALSE).
y_scale_mannual: Logical value indicating whether to manually specify y-axis limits (default is FALSE).
linetype: The line type for significance thresholds (default is 4).
line.alpha: The transparency level for significance thresholds (default is 0.4).
line.color: The color for significance thresholds (default is 'grey34').
line.size: The size of significance thresholds (default is 1).
annotation.label: The name of species that need to be annotated (default is NULL).
annotation.color: The color of the annotation points (default is '#C82423')
text.size: The size of gene labels (default is 1.5).
max.overlap: The maximum number of overlapping labels allowed (default is 40).
title: The title for the plot (default is NULL).