Description Usage Arguments Value Examples
View source: R/DI_plot_helpers.R
Plot dissimilarities withing and among sets of selected sites as a dendrogram
1 2 3 4 | DI_dendrogram(DI_selected_sites, selection_type = "selections",
selection_number = 1, labels = NULL, xlab = "",
ylab = "Distance", main = "Cluster dendrogram",
sub = "", ...)
|
DI_selected_sites |
list of results obtained with function
|
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 |
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
" |
A dendrogram plot of a "hclust
" object.
1 2 3 4 5 6 7 8 9 10 11 12 | # Data
data("b_pam", package = "biosurvey")
data("m_selection", 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)
|
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