volcano_plot: Volcano plot

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Draws a volcano plot of effect size and p-values.

Usage

volcano_plot(data, x, p, p_fdr = NULL, color = NULL,
  p_breaks = c(0.05, 0.01, 0.001, 1e-04), fdr_limit = 0.05,
  log2_x = FALSE, center_x_axis = TRUE, x_lim = NULL,
  color_scale = NULL, title = "Volcano plot", subtitle = NULL, ...)

Arguments

data	a data frame with the effect size and p-values
x, p	the column names of effect size (x-axis) and p-values
p_fdr	column name of FDR corrected p-values, used to draw a line showing the fdr-corrected significance level
color	column name used to color the plots
p_breaks	a numerical vector of the p_values to show on the y-axis
fdr_limit	the significance level used in the experiment
log2_x	logical, whether effect size should be plotted on a log2 axis
center_x_axis	logical, whether x-axis should be centered. If TRUE, the "zero-effect" will be on the middle of the plot. The "zero effect" is 0 if log2_x = FALSE and 1 if log2_x = TRUE
x_lim	numerical vector of length 2 for manually setting the x-axis limits
color_scale	the color scale as returned by a ggplot function
title, subtitle	the title and subtitle of the plot
...	parameters passed to geom_point, such as shape and alpha values. New aesthetics can also be passed using mapping = aes(...).

Value

a ggplot object

Examples

# naturally, this looks messy as there are not enough p-values
lm_results <- perform_lm(drop_qcs(merged_sample), formula_char = "Feature ~ Group")
volcano_plot(data = lm_results, x = "GroupB_Estimate",
             p = "GroupB_P", p_fdr = "GroupB_P_FDR",
             fdr_limit = 0.1)

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.