QQ plot for GWAS p-values

Create a quantile-quantile plot with confidence bands and genomic inflation factor.

Usage

qq_plot(
  data,
  p = NULL,
  ci = 0.95,
  ci_fill = "grey80",
  ci_alpha = 0.3,
  show_lambda = TRUE,
  lambda_position = "topleft",
  group = NULL,
  point_size = 0.8,
  point_color = "#1A5276",
  alpha = 1,
  line_color = "#E74C3C",
  downsample = TRUE,
  downsample_n = 1e+05,
  title = NULL
)

Arguments

data

A gwas_data object or data.frame, or a numeric vector of p-values.

p

Column name for p-values (auto-detected if NULL).

ci

Confidence level for bands (NULL to disable).

ci_fill

Fill color for confidence band.

ci_alpha

Transparency of confidence band.

show_lambda

Show genomic inflation factor annotation.

lambda_position

Position for lambda annotation: "topleft" or "bottomright".

group

Column name to stratify QQ plot by groups.

point_size

Point size.

point_color

Point color (ignored if group is specified).

alpha

Point transparency.

line_color

Color of the identity line.

downsample

Enable downsampling of dense lower-left region.

downsample_n

Target number of points.

title

Plot title.

Value

A ggplot object.

Examples

data(example_gwas, package = "ggwas")

# Basic QQ with lambda and confidence band
qq_plot(example_gwas, show_lambda = TRUE, ci = 0.95)


# Without confidence band
qq_plot(example_gwas, show_lambda = TRUE, ci = NULL)


# Stratify by allele frequency
example_gwas$maf_bin <- cut(example_gwas$AF, c(0, 0.05, 0.2, 0.5),
                            labels = c("Rare", "Low", "Common"))
qq_plot(example_gwas, group = "maf_bin")


# Nature theme
qq_plot(example_gwas, show_lambda = TRUE) + theme_nature()