volcano_plot: Volcano plot

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Volcano plot

Description

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

Usage

volcano_plot(
  object,
  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,
  label = NULL,
  label_limit = 0.05,
  color_scale = getOption("notame.color_scale_con"),
  title = "Volcano plot",
  subtitle = NULL,
  text_base_size = 14,
  label_text_size = 4,
  ...
)

Arguments

object	a MetaboSet object or a data frame. If x is a MetaboSet object, fData(x) is used. If x is a data frame, it is used as is.
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
label	column name used to label the plots
label_limit	numeric, p-value which is used to limit label plotting. Defaults to 0.05.
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(lm_results,
  x = "GroupB_Estimate",
  p = "GroupB_P", p_fdr = "GroupB_P_FDR",
  label = "Feature_ID",
  fdr_limit = 0.1
)

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.