plot_pairwise_fst_heatmap: Make an heatmap of pairwise Fst values.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Make an heatmap of pairwise Fst values.

Description

Creates a ggplot heatmap of pairwise Fst values previously calculated via calc_pairwise_fst. Optionally prints Fst values and marks those with significant p-values.

Usage

plot_pairwise_fst_heatmap(
  x,
  facets = NULL,
  facet.order = NULL,
  viridis.option = "inferno",
  print_fst = TRUE,
  mark_sig = FALSE,
  lab_lower = FALSE
)

Arguments

x	snpRdata object.
facets	character, default NULL. Categorical metadata variables by which to break up plots. Must match facets for which Fst data has been previously calculated via calc_pairwise_fst. See Facets_in_snpR for more details.
facet.order	character, default NULL. Optional order in which the levels of the provided facet should appear on the plot, bottom to top/left to right. If multiple facets are plotted, this must be a named list, named by facet, otherwise a character vector. See examples.
viridis.option	character, default "inferno". Viridis color scale option to use. Other color scales may be substituted by appending the scale_color_continuous and scale_fill_continuous ggplot functions to the produced plot using the '+' operator.
print_fst	logical, default TRUE. If true, will print Fst values on plot.
mark_sig	numeric or FALSE, default FALSE. If numeric, Fst values with bootstrapped p-values below the given number will be marked with an '*'. Requires that bootstrapped p-values were calculated for the requested facets.
lab_lower	logical, default FALSE. If TRUE, labels will be placed in the lower triangle instead of on top of the heatmap.

Value

A ggplot or list of named ggplots for each facet.

Author(s)

William Hemstrom

Examples

# Calculate pairwise fst
x <- calc_pairwise_fst(stickSNPs, c("pop", "fam"))

# plot
plot_pairwise_fst_heatmap(x, "pop")

# plot without FST values
plot_pairwise_fst_heatmap(x, "pop", print_fst = FALSE)

# bootstrap some p-values and plot
x <- calc_pairwise_fst(x, "pop", boot = 5)
## using a high alpha due low number of boots
plot_pairwise_fst_heatmap(x, "pop", mark_sig = .2) 

# put labels in lower triangle
plot_pairwise_fst_heatmap(x, "pop", mark_sig = .2, lab_lower = TRUE) 

# provide facet orders
plot_pairwise_fst_heatmap(x, c("pop", "fam"), 
                         list(pop = c("PAL", "ASP", "UPD", 
                                      "CLF", "SMR", "OPL"),
                             fam = c("A", "B", "C", "D")),
                         print_fst = TRUE, lab_lower = TRUE)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.