Code for statistics, NMDS and Heatmap plots

This folder contains R and Jupyter code and data for making statistical analyses and create NMDS and Heatmap figures for EcoFAB 2.0 Ring Trial. "two-way-anova-ecofab-ringtrial-stats.ipynb" generates statistical analysis utilizing RawData from the paper."Heat_KEGG.r" generates combative genomics heat map utilizing normalized KEGG pathway gene abundance in "Heat_KEGG.xlsx" dataset."Heat_TM.r" generates heat map plot for targeted metabolomics utilizing normalized metabolite intensity "Heat_TM.xlsx" dataset"NMDS_UM.r" generates NMDS plots for untargeted metabolomics utilizing raw peak heights for detected features in "NMDS_UM.xlsx" and "NMDS_UM1.xlsx" datasets"NMDS_seq.r" generates NMDS plots for root and media microbiome composition utilizing relative bacterial abundances from 16S rRNA sequencing in "Seq_media.xlsx" and "Seq_root" datasets.