![]() ![]() Plot the rarefaction curves using vegan function rarecurve(): The sampling depth (in m), the month and the year of sampling. The sample data contains 4 features for each sample: the season of sampling, Print the metadata using the phyloseq function sample_data(): Taxonomy for each OTU), the phylogenetic tree, and the OTU representative (containing the metadata for each sample), the taxonomy table (the predicted Table (which contains the OTU counts for each sample), the sample data matrix ![]() The import_biom() function returns a phyloseq object which includes the OTU library ( "phyloseq" ) > library ( "ggplot2" ) > library ( "vegan" ) > library ( "DESeq2" ) > setwd ( "/home/rstudio/micca/garda/denovo_greedy_otus" ) # set the working directory > ps = import_biom ( "tables.biom", treefilename = "tree_ee", refseqfilename = "otus.fasta" ) > sample_data ( ps ) $ Month ps phyloseq - class experiment - level object otu_table () OTU Table : sample_data () Sample Data : tax_table () Taxonomy Table : phy_tree () Phylogenetic Tree : refseq () DNAStringSet : ![]()
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