make.tree: generate a hclust dendrogram

In MRCIEU/metaboprep: Metabolomics data preparation and processing pipeline

generate a hclust dendrogram

Description

This estimates a dendrogram of feautres based on correlation coefficeint of your choice, and a clustering method of choice

Usage

make.tree(wdata, cor_method = "spearman", hclust_method = "complete")

Arguments

wdata	the metabolite data matrix. samples in row, metabolites in columns
cor_method	the correlation method used in the function cor(). Default is "spearman".
hclust_method	the dendrogram clustering method used in the construction of the tree. Default is "complete".

Value

an hclust object

Examples

cmat = matrix(1, 4, 4 )
cmat[1,] = c(1, 0.8, 0.6, 0.2)
cmat[2,] = c(0.8, 1, 0.7, 0.5)
cmat[3,] = c(0.6, 0.7, 1, 0.6)
cmat[4,] = c(0.2, 0.5, 0.6,1)
## simulate some correlated data (multivariable random normal)
set.seed(1110)
ex_data = MASS::mvrnorm(n = 250, mu = c(5, 45, 25, 15), Sigma = cmat )
## estiamte the dendrogram
tree = make.tree(ex_data)
## plot the dendrogram
plot(tree, hang = -1)

MRCIEU/metaboprep documentation built on Jan. 28, 2023, 7:29 p.m.