manhattan_plot: Manhattan plot

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Draws a (directed) Manhattan plot of p-values and versus e.g. retention time or mass-to-charge ratio. If effect size and direction is supplied, the -log10(p-value) on the y-axis will be multiplied by the direction (sign) of the effect, so part of the points will "drop" from the p = 1 (-log10(p) = 0) line. This results in a so-called directed Manhattan plot.

Usage

manhattan_plot(data, x, p, effect = NULL, p_fdr = NULL, color = NULL,
  p_breaks = c(0.05, 0.01, 0.001, 1e-04), fdr_limit = 0.05,
  x_lim = NULL, y_lim = NULL, color_scale = NULL,
  title = "Manhattan 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
effect	column name of effect size (should have negative and positive 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
x_lim, ylim	numerical vectors of length 2 for manually setting the 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")
lm_data <- dplyr::left_join(fData(merged_sample), lm_results)
# Traditional Manhattan plot
manhattan_plot(data = lm_data, x = "Average.Mz",
             p = "GroupB_P", p_fdr = "GroupB_P_FDR",
             fdr_limit = 0.1)
# Directed Manhattan plot
manhattan_plot(data = lm_data, x = "Average.Mz", effect = "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.