PluMA plugin that outputs various statistics on core communities of taxa in a set of samples.
The following are specified in the input TXT file, as tab-delimited keyword-value pairs.
otufile: OTU abundances (CSV) mapping: Mapping table (CSV) tree: Phylogenetic tree (CSV) column: (STRING) detection: Minimum relative abundance to be counted at all (REAL) prevalence: Minimum relative abundance to be counted as core
The output prefix will be used for three files: prefix.members.csv: Core taxa prefix.abundindex.csv: Percentage of each sample that is a core community prefix.coverage.csv: Amount of core taxa sequences in each sample
Format of the otufile CSV:
- Rows are OTUs, columns are samples
- Entry (i,j) is the abundance of OTU in sample j. Can be absolute or relative.
Format of the mapping CSV:
- Rows are samples, columns are metadata
- One single header row, i.e: sample,subject,visit
Format of the tree CSV;
- Rows are OTUs, columns are classifications
- One single header row, i.e. OTU,Kingdom,Phylum,Class,Order,Family,Genus,Species