R code
Loading packages & data
library(scales)
library(ape)
source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R")
#if in new session
#library(phyloseq)
#data <- path to Rdata file
#load(data)
##get dist object from distance matrix file
distance <- # path to Beta diversity tsv file
A <- read.table(file=distance, row.names=1)
dist <- as.dist(A)
## Env types
varExp <- # (discrete) experimental variable used to color samples
Sample clustering using different linkage method
plot_clust(data, dist, method = "ward.D2", color = varExp)
plot_clust(data, dist, method = "complete", color = varExp)
plot_clust(data, dist, method = "single", color = varExp)
library(scales)
library(ape)
#if in new session
#library(phyloseq)
#source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R
")
#data <- path to Rdata file
#load(data)
##get dist object from distance matrix file
distance <- # path to Beta diversity tsv file
A <- read.table(file=distance, row.names=1)
dist <- as.dist(A)
## Env types
varExp <- #(discrete) experimental variable used to color samples
## Clustering Trees
plot_clust(data, dist, method = "ward.D2", color = varExp)
plot_clust(data, dist, method = "complete", color = varExp)
plot_clust(data, dist, method = "single", color = varExp)