heatmap_fst — heatmap_fst • assigner

Function that generate an Heatmap of Fst and CI values

Usage

heatmap_fst(
  pairwise.fst = NULL,
  pairwise.fst.full.matrix = NULL,
  pairwise.fst.ci.matrix = NULL,
  pop.levels = NULL,
  n.s = TRUE,
  digits = 5,
  color.low = "blue",
  color.mid = "yellow",
  color.high = "red",
  text.size = 4,
  plot.size = NULL,
  path.folder = NULL,
  filename = NULL
)

Arguments

pairwise.fst: (object or path). Tibble with all the info generated by fst_WC84. If this is not used, pairwise.fst.full.matrix and pairwise.fst.ci.matrix are both required.
pairwise.fst.full.matrix: (object or path).
pairwise.fst.ci.matrix: (object or path).
pop.levels: (optional, character, string) If not supplied, the order is set from the colnames of the full fst matrix. Default: pop.levels = NULL.
n.s: (optional, logical) To have an * when the Fst value is not significant (0 is the lower bound of the CI). Default: n.s = TRUE.
digits: (optional, integer) The number of digits showed in the heatmap. Default: digits = 5.
color.low: (optional, character) Color of lower bound. Default: color.low = "blue".
color.mid: (optional, character) Mid color value. Default: color.mid = "yellow".
color.high: (optional, character) Color of higher bound. Default: color.high = "red".
text.size: (optional, integer) Size of the values. Default: text.size = 2.
plot.size: (optional, integer) By default the size is the number of strata * 2 in cm. Default: plot.size = NULL.
path.folder: (optional, character) Default: path.folder = NULL. Default will use the working directory.
filename: (optional, character) Name of the plot to write. Default: filename = NULL. With default, the plot is not written to disk.