Draw extended plot of summary statistics for two coloc datasets

Source: R/plot.R

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.

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

Value

a gtable object

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.

Author

Tom Willis

Examples

if (FALSE) { # \dontrun{
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"))
} # }