fast_qq: A fast version of a quantile-quantile plot

In roman-tremmel/ggfastman: ggfastman: ggplot2-based manhattenplots in fast and ultrafast

A fast version of a quantile-quantile plot

Description

This is a very fast plotting function for quantile-quantile (QQ) plots using ggplot2 and scattermore functionalities.

Usage

fast_qq(
  pvalue,
  speed = "fast",
  pointsize = 1.2,
  linecolor = "deeppink",
  ci_color = "steelblue",
  ci_alpha = 0.3,
  conf.alpha = 0.05,
  confint = T,
  log10 = T,
  inflation_method = "median",
  title = "QQ-plot"
)

Arguments

pvalue	A numeric vector of pvalues.
speed	The speed option. Fast and ultrafast use scattermore functionality
pointsize	Only when using the 'fast' option you can increase pointsize. Default is 1.2
linecolor	Color of the abline of the theoretical and sample distributions.
ci_color	Color fof the confidence interval
ci_alpha	Alpha value (e.g. transparency) of the confidence's fill color
conf.alpha	Alpha level of the confidence interval. Default value = 0.05
confint	Print a confident interval. Default = TRUE
log10	Should the pvalues -log10 tranformed? Default = TRUE
inflation_method	Method to calculate the genomic inflation factor. choices = c("median","regression"). The "median" method is the most common way to estimate lambda. The regression method is adapted from the GenABEL package.
title	A title added to the plot

Value

A ggplot2 object/plot

Examples

data("gwas_data")
head(gwas_data)
fast_qq(gwas_data$pvalue, inflation_method = "reg")
fast_qq(gwas_data$pvalue, inflation_method = "med")

roman-tremmel/ggfastman documentation built on Feb. 20, 2024, 11:59 a.m.