Data overview:
ps.RData = original phyloseq object ps_clean_no_ctrl.RData = uses ps.RData to remove controls ps_1126.RData = ps_rare.RData = rarefied ps_1126 for alpha diversity ps_filtered.RData = removes low read samples _331 and _333 ps_rel.RData = normalised ps_filtered file by calculating the relative abundance of all the samples
Scripts overview:
Piechart_script.R = to be used in automatic report generation, creates pie charts for showing composition (Phylum/Family) in samples per zoo.
Rarefaction.R = rarefies data, results in ps_filtered, ps_rel and ps_rare files.
Relative_Abundance.R = Uses ps_rel to normalise data and generate relative abundance in sample per zoo, also creates relative abundance plot for merged samples by zoo