snplinkage (version 1.2.0)

gtable_ld: 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 = "",
  ...
)

Value

gtable of ggplots

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

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))