volcano {LipidomicsR}

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
)

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).

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.