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Plot delNero2022 Catchment Areas

Source: R/plot_delNero2022_catchment_areas.R
plot_delNero2022_catchment_areas.Rd

This function generates a plot of the delNero2022 catchment areas, showing the adjusted genotypic frequency (GF) for a specified allele across the National Cancer Institute (NCI) catchment areas in the continental United States.

Usage

plot_delNero2022_catchment_areas(
  query_allele,
 
    sf_tract_centroids_for_all_states_with_catchment_with_us_population_race_code_percentages_by_tract_summed
)

Arguments

query_allele

A character string specifying the allele to plot (e.g., "A*11:01").

sf_tract_centroids_for_all_states_with_catchment_with_us_population_race_code_percentages_by_tract_summed

A spatial data frame containing tract centroids for all states, including catchment areas and US population race code percentages by tract, summed for the analysis.

Value

A ggplot2 object representing the plot of the catchment areas with the genotypic frequency for the specified allele.

Details

  • The function uses the rnaturalearth package to retrieve state boundaries and filters out non-continental states (e.g., Hawaii, Alaska, and territories).

  • The coordinate reference system (CRS) is transformed to match the census data (EPSG: 4269).

  • The plot includes a base map of the continental United States and overlays the catchment areas with the genotypic frequency data.

  • The viridis color scale is used for better visualization of the genotypic frequency.

Examples

if (FALSE) { # \dontrun{
# Example usage:
plot_delNero2022_catchment_areas(
  query_allele = 'A*11:01',
  sf_tract_centroids_for_all_states_with_catchment_with_us_population_race_code_percentages_by_tract_summed = your_data
)
} # }