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Create a regional association plot

Source: R/gg_locusplot.R
gg_locusplot.Rd

Returns a ggplot object containing a regional association plot (-log10(p-value) as a function of chromosomal position, with variants colored by linkage disequilibrium to reference variant). This function allows the user to integrate genome wide association study (GWAS) summary statistics for a locus of interest with linkage disequilibrium information (obtained using the University of Michigan LocusZoom API https://portaldev.sph.umich.edu/) for that locus to create a regional association plot.

Usage

gg_locusplot(
  df,
  lead_snp = NULL,
  rsid = rsid,
  chrom = chrom,
  pos = pos,
  ref = ref,
  alt = alt,
  effect = NULL,
  std_err = NULL,
  p_value = p_value,
  trait = NULL,
  plot_pvalue_threshold = 0.1,
  plot_subsample_prop = 0.25,
  plot_distance = 5e+05,
  genome_build = "GRCh37",
  population = "ALL",
  plot_genes = FALSE,
  plot_recombination = FALSE,
  plot_title = NULL,
  plot_subtitle = NULL,
  path = NULL
)

Arguments

df

Dataframe containing columns with rsid, chromosome, position, reference/effect allele, alternate/non-effect allele, and p-value for all variants within the range of interest

lead_snp

A character vector containing a lead variant of interest. When NULL (default), the variant with the lowest p-value will be selected as the lead variant.

rsid

Rsid column

chrom

Chromosome column

pos

Position column

ref

Reference/effect allele column

alt

Alternate/non-effect allele column

effect

Effect size column (on beta or log-odds scale)

std_err

Standard error column

p_value

P-value column

trait

(optional) Column containing the name of the trait

plot_pvalue_threshold

Threshold for plotting p-value on regional association plot (default = 0.1) - reducing the number of points decreases file size and improves performance

plot_subsample_prop

Proportion of points above p-value threshold to plot (default = 0.25; range = 0-1) - reducing the number of points decreases file size and improves performance

plot_distance

Integer corresponding to the size of the locus that should be plotted

genome_build

Character - one of "GRCh37" or "GRCh38"

population

Character - one of "ALL", "AFR", "AMR", "EAS", "EUR", "SAS" referring to the reference population of interest for obtaining linkage disequilibrium information (default = "ALL")

plot_genes

Logical - Include a plot of genes/transcripts within the region of interest beneath the regional association plot (default = FALSE)

plot_recombination

Logical - Include a secondary y-axis of recombination rate within the region of interest

plot_title

A character string corresponding to plot title (default = NULL)

plot_subtitle

A character string corresponding to plot subtitle (default = NULL)

path

Character string (default = NULL) - if a path is supplied a .pdf of the plot will be saved

Value

A ggplot object containing a regional association plot for the locus of interest

Examples

if (FALSE) { # \dontrun{
# Basic regional association plot
gg_locusplot(df = fto_locus_df, lead_snp = "rs62033413", rsid = rsid, chrom = chromosome, pos = position, ref = effect_allele, alt = other_allele, p_value = p_value)

# Use "plot_genes = TRUE" to add a plot of genes within the region beneath the regional association plot
gg_locusplot(df = fto_locus_df, lead_snp = "rs62033413", rsid = rsid, chrom = chromosome, pos = position, ref = effect_allele, alt = other_allele, p_value = p_value, plot_genes = TRUE)
} # }