find.hclust: find the hierarchical cluster analysis among the nodes of...

In YuLab-SMU/treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.

Description

find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.

Usage

find.hclust(
  x,
  graph.mst = FALSE,
  weights = NULL,
  hclust.method = "average",
  ...
)

Arguments

x	a igraph object
graph.mst	logical whether obtain the minimum spanning tree first then find.hclust, default is FALSE.
weights	a numeric vector giving edge weights or a character. If this is NULL and the graph has a weight edge attribute, then the attribute is used. If this is NA then no weights are used even if the graph has a weight attribute. If this is a character, the graph has the edge attribute which is numeric, then it will be used, default is NULL.
hclust.method	the agglomeration method to be used, This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
...	additional parameters

Value

hclust object

Examples

library(igraph)
set.seed(123)
g <- igraph::sample_gnp(100, .1) %>%
     set_edge_attr(name='weight', value=abs(rnorm(E(.),3)))
tr1 <- find.hclust(g, weights = NA)
tr2 <- find.hclust(g)
tr3 <- find.hclust(g, graph.mst = TRUE)

YuLab-SMU/treeio documentation built on Nov. 3, 2024, 4:17 p.m.