Build an UPGMA or neighbour-joining tree from a square pairwise FST matrix, optionally estimate bootstrap support, and draw the result with `ggtree`.
Usage
plot_fst_tree(
data,
tree.method = c("upgma", "nj"),
bootstrap = 1000L,
scale = TRUE,
ladderize = FALSE,
xlim = NULL,
plot.name = "tree",
tree.width = 15,
tree.height = 15
)Arguments
- data
A numeric, square, symmetric pairwise FST matrix with matching, non-empty row and column names.
- tree.method
Clustering method: `"upgma"` or `"nj"`.
- bootstrap
Number of bootstrap replicates. Use `NULL` or a value below three to skip bootstrapping.
- scale
Logical; display a tree scale bar.
- ladderize
Logical; ladderize the displayed tree.
- xlim
Optional numeric vector of length two passed to [ggplot2::xlim()]. Use `NULL` to let ggplot2 choose the limits.
- plot.name
Output filename stem. When `NULL`, files are not written.
- tree.width, tree.height
Output dimensions in centimetres.
Value
A `ggtree` plot. The underlying `phylo` object and bootstrap support are available in the plot attributes `tree` and `bootstrap`.
References
Yu G (2020). Using ggtree to visualize data on tree-like structures. *Current Protocols in Bioinformatics*, 69, e96.
Examples
if (FALSE) { # \dontrun{
fit <- fst_WC84(data)
plot_fst_tree(
data = fit$pairwise.fst.full.matrix,
plot.name = "population_tree",
bootstrap = 1000L
)
} # }