plot_phewas: Plot 'PheWAS()' results.

In otargen: Access Open Target Genetics

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")
)

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.

Value

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

Examples

## Not run: 
p <- pheWAS(variant_id = "14_87978408_G_A") %>%
     plot_phewas(disease = TRUE)
p

## End(Not run)

otargen documentation built on Sept. 30, 2024, 9:43 a.m.