Plot assembly clustering dendrogram — plot_dendro • paneffectR

Clusters assemblies by shared orthogroup content and displays as a dendrogram.

Usage

plot_dendro(
  pa,
  distance_method = "jaccard",
  cluster_method = "complete",
  labels = TRUE,
  hang = 0.1
)

Arguments

pa: A pa_matrix object.
distance_method: Character. Distance metric: "jaccard" (default), "binary", or "bray-curtis".
cluster_method: Character. Clustering method for hclust (default: "complete"). Options: "complete", "single", "average", "ward.D2".
labels: Logical. Whether to show assembly labels (default: TRUE).
hang: Numeric. Fraction of plot height to hang labels below leaves (default: 0.1).

Value

A ggplot2 object.

Examples

if (FALSE) { # \dontrun{
plot_dendro(pa)
plot_dendro(pa, distance_method = "bray-curtis")
plot_dendro(pa, cluster_method = "ward.D2")
} # }