gtable_ld: Gtable of linkage disequilibrium and chromosomic positions

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Gtable of linkage disequilibrium and chromosomic positions

Description

Creates a gtable of linkage disequilibrium and chromosomic positions ggplots. A biplot_subset parameter is available to add a second linkage disequibrium ggplot to visualize the effect of a SNP selection.

Usage

gtable_ld(
  df_ld,
  df_snp,
  biplot_subset = NULL,
  labels_colname = NULL,
  diamonds = length(unique(df_ld$SNP_A)) < 40,
  point_size = ifelse(is.null(biplot_subset), 120, 80)/sqrt(nrow(df_ld)),
  title = "",
  title_biplot = "",
  ...
)

Arguments

df_ld	Data frame returned by snprelate_ld
df_snp	SNP annotations with columns snpID and position
biplot_subset	SNP indexes of the subset for the second ld plot
labels_colname	Column name of df_snp to use as SNP labels
diamonds	Display the values as diamonds or as points Default is TRUE for less than 40 SNPs.
point_size	Size for geom_point. Ignored if diamonds is TRUE.
title	Plot title
title_biplot	Optional biplot title
...	Passed to ggplot_ld

Value

gtable of ggplots

Examples

library(snplinkage)
gds_path <- save_hgdp_as_gds()
gdata <- load_gds_as_genotype_data(gds_path)
qc <- snprelate_qc(gdata, tagsnp = .99)
snp_idxs_8p23 <- select_region_idxs(qc$gdata, chromosome = 8,
  position_min = 11e6, position_max = 12e6)

df_ld <- snprelate_ld(qc$gdata, snps_idx = snp_idxs_8p23, quiet = TRUE)
plt <- gtable_ld(df_ld, df_snp = gdata_snps_annots(qc$gdata))

snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.