2 Testing Microbial Community Composition

This section delves into statistical analysis methods tailored specifically for microbiome data. Statistical analysis plays a crucial role in understanding the complex relationships and patterns within microbiome datasets, helping researchers uncover significant findings and insights into microbial community dynamics, composition, and responses to various environmental factors or treatments.

knitr::opts_chunk$set(
  echo  =TRUE,
  message  =FALSE,
  warning  =FALSE,
  cache  =FALSE,
  comment  =NA,
  collapse =TRUE,
  fig.path='./figures/',
  fig.show='asis',
  dev  ='png')

2.1 Load processed data objects

# Load required packages
library(phyloseq)
library(tidyverse)
library(microbial)
library(microbiome)
library(microViz)

load("../imap-data-exploration/data/psextra_distances.rda", verbose = T)
Loading objects:
  psextra_clr_asin_bray_dist
  psextra_id_asin_bray_dist
  psextra_log10p_asin_bray_dist
load("../imap-data-exploration/data/phyloseq_raw_rel_psextra_df_objects.rda", verbose = T)
Loading objects:
  ps_raw
  ps_rel
  psextra_raw
  psextra_rel
  ps_df