Autoplots for gt_pcadapt objects — autoplot_gt

For gt_pcadapt, the following types of plots are available:

qq: a quantile-quantile plot of the p-values from pcadapt (wrapping bigsnpr::snp_qq())
manhattan a manhattan plot of the p-values from pcadapt (wrapping bigsnpr::snp_manhattan())

Usage

# S3 method for class 'gt_pcadapt'
autoplot(object, type = c("qq", "manhattan"), ...)

Arguments

object: an object of class gt_pcadapt
type: the type of plot (one of "qq", and "manhattan")
...: further arguments to be passed to bigsnpr::snp_qq() or bigsnpr::snp_manhattan().

Value

a ggplot2 object

Details

autoplot produces simple plots to quickly inspect an object. They are not customisable; we recommend that you use ggplot2 to produce publication ready plots.

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 object
pca <- gt_pca_partialSVD(lobsters)

# Create a gt_pcadapt object
pcadapt_obj <- gt_pcadapt(lobsters, pca, k = 2)

# Plot the p-values from pcadapt
autoplot(pcadapt_obj, type = "qq")


# Plot the manhattan plot of the p-values from pcadapt
autoplot(pcadapt_obj, type = "manhattan")