plot_qqman {omixVizR} | R Documentation |
plot_qqman
Description
Create GWAS QQ & Manhattan Plots.
Usage
plot_qqman(
plink_assoc_file,
pheno_name,
maf_filter = NULL,
output_graphics = "png",
save_plot = TRUE
)
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 |
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
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.")
}