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