otargen (version 1.1.5)

plot_phewas: Plot PheWAS() results.

Description

This plot visualizes which traits are associated with the user's selected variant in the UK Biobank, FinnGen, and/or GWAS Catalog summary statistics repository based on PheWAS analysis. The associated traits are mapped onto the x-axis, and their corresponding -log10(p-value) values are plotted on the y-axis. A horizontal line is shown at a p-value cutoff of 0.005 to indicate significant associations. Associations above this cutoff are labeled with the trait's name, and the sources of the associations are color-coded as points.

Usage

plot_phewas(
  data,
  disease = TRUE,
  source = c("GCST", "FINNGEN", "NEALE", "SAIGE")
)

Value

A plot to prioritize variants based on their -log10(p-value).

Arguments

data

Data Frame: The result of the PheWAS() function in data frame format, containing the PheWAS information for a selected variant ID.

disease

Logical: A logical variable indicating whether to filter the PheWAS data for disease (default: TRUE).

source

Character vector: Choices for the data sources of PheWAS analysis, including FINNGEN, GCST, NEALE (UKBiobank), and SAIGE.

Examples

if (FALSE) {
p <- pheWAS(variant_id = "14_87978408_G_A") %>%
     plot_phewas(disease = TRUE)
p
}