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)
#> Running analysis...
#> Random selection
#> 	One or more sites were excluded due to lack of species data:
#> 	Site_15
#> G selection
#> 	One or more sites were excluded due to lack of species data:
#> 	Site_4, Site_10, Site_19, Site_20
#> E selection
#> Summary of all selections

# Plot
DI_dendrogram(DI_sel)