plot_qqman {omixVizR}R Documentation

Plot GWAS QQ and Manhattan Plots

Description

Create GWAS QQ & Manhattan Plots.

Usage

plot_qqman(
  plink_assoc_file,
  pheno_name,
  maf_filter = NULL,
  output_graphics = "png",
  save_plot = TRUE,
  lambda1_qq_pos = c(2.1, -5.5),
  lambda2_qq_pos = c(1.565, -4)
)

Arguments

plink_assoc_file

Path to the PLINK association file.

pheno_name

Phenotype name.

maf_filter

Minor allele frequency filter, Default: NULL

output_graphics

Output graphics format, Default: 'png'

save_plot

Logical, whether to save plots to files. If FALSE, plots are only displayed. Default: TRUE

lambda1_qq_pos

A numeric vector of length 2 specifying the c(hjust, vjust) for the lambda text in the QQ plot. Default: c(2.1, -5.5).

lambda2_qq_pos

A numeric vector of length 2 specifying the c(hjust, vjust) for the SNP count (N) text in the QQ plot. Default: c(1.565, -4.0).

Details

This function reads a PLINK association file and generates Manhattan and QQ plots for the GWAS results.

Value

A list containing the ggplot objects for the Manhattan and QQ plots.

Font Information

The MetroSans font included in this package is sourced from https://fontshub.pro/font/metro-sans-download#google_vignette. It is intended for academic research and non-commercial use only. For commercial use, please contact the font copyright holder.

The font files are included in the package's inst/extdata directory and are automatically loaded for plotting.

Author(s)

Zhen Lu luzh29@mail2.sysu.edu.cn

Yanhong Liu liuyh275@mail2.sysu.edu.cn

Siyang Liu liusy99@mail.sysu.edu.cn

See Also

lulab.utils

Examples


  sample_file <- system.file("extdata", "sample_gwas.assoc.linear", package = "omixVizR")
  
  # Check if the file exists before running the example
  if (file.exists(sample_file)) {
    # Run the function with the sample data
    plots <- plot_qqman(
      plink_assoc_file = sample_file,
      pheno_name = "SamplePheno",
      save_plot = FALSE
    )
    # You can then access the plots like this:
    # print(plots$manhattan_plot)
    # print(plots$qq_plot)
  } else {
    message("Sample file not found, skipping example.")
  }


[Package omixVizR version 1.1.3 Index]