refdb_plot_tax_tree: Reference database taxonomy tree

In refdb: A DNA Reference Library Manager

Reference database taxonomy tree

Description

Represent the hierarchical structure of the taxonomic information of a reference database as a tree.

Usage

refdb_plot_tax_tree(
  x,
  leaf_col = NULL,
  color_col = NULL,
  freq_labels = 0,
  expand_plot = 0.5
)

Arguments

x	a reference database.
leaf_col	a column name referring to the taxonomic level for the leaves of the tree. If not provided (NULL) the function tries to find a relevant level.
color_col	a column name referring to the taxonomic level for the color of the leaves (must be higher or equal to the level of leaf_col). If not provided (NULL) the function tries to find a relevant level.
freq_labels	a numeric value to adjust the number of printed labels (minimum frequency). Default is zero which means all non-NA labels are printed.
expand_plot	a value to expand the limits of the plot. Useful if the labels are too long.

Details

The underlying graph is computed using the non-exported function igraph_from_taxo.

Value

A ggplot2 (ggraph) object. This means the plot can be further customized using ggplot2 compatible functions.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_plot_tax_tree(lib)

refdb documentation built on Sept. 22, 2022, 5:07 p.m.