#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

metadir=/data/mramseylab/metadata/plaque_meta_4.tsv
visdir=/data/mramseylab/visualizations/AL_2022
procdir=/data/mramseylab/proc_reads/Master-Filtered/
cmr="master-core-metrics-results-HAvPS"

module load QIIME2/2019.7

    qiime longitudinal pairwise-distances \
  --i-distance-matrix $procdir$cmr/bray_curtis_distance_matrix.qza \
  --m-metadata-file $metadir \
  --p-group-column subject \
  --p-state-column environmental-setting \
  --p-state-1 hydroxyapatite \
  --p-state-2 polystyrene \
  --p-individual-id-column sample-name \
  --p-replicate-handling random \
  --o-visualization $visdir/pairwise-distances-AL.qzv


  # generates interactive line plots that allow us to assess how volatile
  #a dependent variable is over a continuous, independent variable (e.g., time) in one or more groups