Plot genomic weighted FST heatmap — plot_snp

Plot genomic weighted FST heatmap.

Usage

plot_snp_fst(
  fst_file,
  bin_size = 1e+06,
  metric = "fst_mean",
  orientation = "horizontal",
  palette = c("#ffffff", "#aa00aa"),
  alpha = 0.9
)

Arguments

fst_file: FST sliding window results. (CHROM, BIN_START, BIN_END, WEIGHTED_FST, N_VARIANTS.
bin_size: Bin size in base pairs. (1e6).
metric: Aggregation metric for bin fill. ("fst_mean", "variant_count").
orientation: Coordinate orientation. ("horizontal", "vertical").
palette: Continuous color for weighted FST. (c("#ffffff", "#aa00aa")).
alpha: Tile alpha for heatmap. (0.9).

Value

A ggplot object showing genomic weighted FST heatmap.

Author

benben-miao

Examples

# Example FST sliding window table in GAnnoViz
fst_file <- system.file(
  "extdata",
  "example.fst",
  package = "GAnnoViz")

# Plot weighted FST
plot_snp_fst(
  fst_file = fst_file,
  bin_size = 1e6,
  metric = "fst_mean",
  orientation = "horizontal",
  palette = c("#ffffff", "#aa00aa"),
  alpha = 0.9
)
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.