plot_extended_dataset: Draw extended plot of summary statistics for two coloc...

In chr1swallace/coloc: Colocalisation Tests of Two Genetic Traits

Draw extended plot of summary statistics for two coloc datasets

Description

Draw Manhattan-style locus plots for p-values in each dataset, gene annotations, a scatter plot of z-scores, and a table of coloc summary statistics.

Usage

plot_extended_dataset(
  dataset1,
  dataset2,
  x,
  first_highlight_list = NULL,
  second_highlight_list = NULL,
  first_index_snp = NULL,
  second_index_snp = NULL,
  first_trait = "Trait 1",
  second_trait = "Trait 2",
  snp_label = "snp",
  ld_label = NULL,
  show_ld = FALSE,
  locus_plot_ylim = NULL,
  ens_db = "EnsDb.Hsapiens.v86"
)

Arguments

x	object of class coloc_abf returned by coloc.abf()
first_highlight_list	character vector of snps to highlight in the first dataset; 'index' can be passed to highlight the most significant SNP
second_highlight_list	character vector of snps to highlight in the second dataset; 'index' can be passed to highlight the most significant SNP
first_index_snp	snp to designate as index snp in the first dataset for the purpose of LD visualisation
second_index_snp	snp to designate as index snp in the second dataset for the purpose of LD visualisation
first_trait	label for the first trait
second_trait	label for the second trait
snp_label	label for the snp column
ld_label	label for the LD column
show_ld	logical, whether to show LD in the locus plots
locus_plot_ylim	numeric vector of length 2 specifying the y-axis limits for the locus plots on the -log10 scale
ens_db	character string specifying Ensembl database package from which to get gene positions. Current (at time of writing this documentation!) sensible values are "EnsDb.Hsapiens.v86" for build 38 and "EnsDb.Hsapiens.v75" for build 37.
d	a coloc dataset

Details

Plot a pair of coloc datasets in an extended format

This function expects that the first two elements of the coloc dataset list d contain summary statistics. Columns labelled 'chromosome', 'position', and 'p' (p-values) are expected in each dataset. The packages locuszoomr and one of EnsDb.Hsapiens.v86 or EnsDb.Hsapiens.v75 are required for this function. One of the EnsDb.Hsapiens libraries containing the Ensembl database specified by ens_db must be loaded prior to use (see the example). EnsDb.Hsapiens.v86 is the default database (GRCh38/hg19); for GRCh37/hg19, use EnsDb.Hsapiens.v75.

Value

a gtable object

Author(s)

Tom Willis

Examples

## Not run: 
library(coloc)
library(EnsDb.Hsapiens.v86)
plot(plot_extended_dataset(list(first_dataset, second_dataset), coloc,
first_highlight_list = c("rs123", "rs456"), 
second_highlight_list = c("rs789", "rs1011"), 
ens_db = "EnsDb.Hsapiens.v86"))

## End(Not run)

chr1swallace/coloc documentation built on June 11, 2025, 7:50 a.m.