augment_loci_gt_pca: Augment the loci table with information from a gt_pca object

In tidypopgen: Tidy Population Genetics

Augment the loci table with information from a gt_pca object

Description

Augment for gt_pca accepts a model object and a gen_tibble and adds loadings for each locus to the loci table. Loadings for each component are stored in a separate column, which is given name with the pattern ".loadingPC1", ".loadingPC2", etc. If data is missing, then a tibble with the loadings is returned.

Usage

## S3 method for class 'gt_pca'
augment_loci(x, data = NULL, k = NULL, ...)

Arguments

x	A gt_pca object returned by one of the ⁠gt_pca_*⁠ functions.
data	the gen_tibble used to run the PCA.
k	the number of components to add
...	Not used. Needed to match generic signature only.

Value

A gen_tibble with a loadings added to the loci tibble (accessible with show_loci(). If data is missing, a tibble of loadings.

See Also

gt_pca_autoSVD() gt_pca_tidiers

Examples

# Create a gen_tibble of lobster genotypes
bed_file <-
  system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
lobsters <- gen_tibble(bed_file,
  backingfile = tempfile("lobsters"),
  quiet = TRUE
)

# Remove monomorphic loci and impute
lobsters <- lobsters %>% select_loci_if(loci_maf(genotypes) > 0)
lobsters <- gt_impute_simple(lobsters, method = "mode")

# Create PCA
pca <- gt_pca_partialSVD(lobsters)

# Augment the gen_tibble with the PCA scores
augment_loci(pca, data = lobsters)

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.