DI_dendrogram: Plot dissimilarities withing and among sets of selected sites...

In claununez/biosurvey: Tools for Biological Survey Planning

Plot dissimilarities withing and among sets of selected sites as a dendrogram

Description

Plot dissimilarities withing and among sets of selected sites as a dendrogram

Usage

DI_dendrogram(DI_selected_sites, selection_type = "selections",
              selection_number = 1, labels = NULL, xlab = "",
              ylab = "Distance", main = "Cluster dendrogram",
              sub = "", ...)

Arguments

DI_selected_sites	list of results obtained with function selected_sites_DI.
selection_type	type of selection to be considered when creating DI matrix plot. Options are: "selections", "random", "E", "G", and "EG". The default, "selections", plots a comparison among all selection types.
selection_number	(numeric) number of selection to be plotted. Default = 1. Ignored if selection_type = "selections".
labels	(character) vector of labels for the tips of the tree. The default, NULL, uses names of sets of selected sites. If labels = FALSE no tip labels are plotted.
xlab	(character) label for x-axis of plot. Default = "".
ylab	(character) label for y-axis of plot. Default = "Distance".
main	(character) title for the plot. Default = "Cluster dendrogram".
sub	(character) subtitle for the plot. Plotted below the label of the x-axis.
...	other arguments to be passed to plot method for objects of class "hclust". See more details in hclust.

Value

A dendrogram plot of a "hclust" object.

Examples

# Data
b_pam <- read_PAM(system.file("extdata/b_pam.rds",
                              package = "biosurvey"))
m_selection <- read_master(system.file("extdata/m_selection.rds",
                                       package = "biosurvey"))

# Subsetting base PAM according to selections
sub_pam_all <- subset_PAM(b_pam, m_selection, selection_type = "all")

# Calculating dissimilarities
DI_sel <- selected_sites_DI(sub_pam_all)

# Plot
DI_dendrogram(DI_sel)

claununez/biosurvey documentation built on April 25, 2024, 12:24 a.m.