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Create a Region Plot with Genetic Data and Recombination Rates

gg_regionplot.Rd

This function generates a region plot with genetic data for a given chromosome and position range, and overlays it with recombination rates. Significant genetic variants are highlighted with labels, and a gene plot is included below the main plot.

Usage

gg_regionplot(
  df,
  rsid,
  chrom,
  pos,
  p_value,
  label = NULL,
  labels = TRUE,
  trait = NULL,
  plot_pvalue_threshold = 0.1,
  genome_build = "GRCh38",
  population = "EUR",
  plot_title = NULL,
  plot_subtitle = NULL
)

Arguments

df

A data frame containing genetic data. It must include the following columns:

  • SNP: SNP identifier (rsid).

  • CHR: Chromosome number.

  • pos: Position of the SNP (e.g., in base pairs).

  • EA: Effect allele (ref).

  • OA: Other allele (alt).

  • phenotype: The trait or phenotype associated with the SNP.

  • p_value: P-value for the association.

rsid

A character vector of SNP identifiers to label on the plot.

chrom

The chromosome number to be used for plotting.

pos

The column name that contains the SNP positions.

p_value

The column name containing the p-values for each SNP.

label

A character vector of SNPs to label on the plot. Default is NULL.

labels

Logical for whether to show text labels for label SNPs

trait

The trait associated with the SNP. Default is NULL.

plot_pvalue_threshold

The p-value threshold for plotting. SNPs with p-values greater than this threshold are excluded from the plot. Default is 0.1.

genome_build

The genome build used for the data (e.g., "GRCh38"). Default is "GRCh38".

population

The population for which the data was analyzed. Default is "EUR".

plot_title

The title of the plot. Default is NULL.

plot_subtitle

The subtitle of the plot. Default is NULL.

Value

A ggplot2 object containing the combined plot of region data with genetic variants, recombination rates, and gene annotations.

Examples

# Example usage
if (FALSE) { # \dontrun{
gg_regionplot(
  df = my_data,
  rsid = c("rs12345", "rs67890"),
  chrom = 1,
  pos = "position",
  p_value = "p_value",
  label = c("rs12345"),
  plot_title = "Region Plot Example"
)
} # }