MakeEDABargraphs: Function to automatically generate a few Phyloseq bargraphs...

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

Description

This function uses a shared file (i.e. a mothur-formatted OTU contingency table) and a taxonomy file (i.e. an RDP naive bayesian fixed-rank asignment detail) to generate three stacked barcharts in the folder it is executed in. The function returns a phyloseq object as well by default.

Usage

MakeEDABargraphs(shared, taxonomy, retfphyloseq = TRUE)

Arguments

shared	file location string for the shared file (preferably absolute path)
taxonomy	file location string for the taxonomy file (preferably absolute path)
retfphyloseq	wheter or not to return a phyloseq object (defaults to true)

Value

A phyloseq object and three plots in the current directory

Examples

shareddataset <- system.file("extdata","large_shared_file.shared",
                              package = "CMETNGS",mustWork = TRUE)
taxonomydataset <- system.file("extdata","large_OTU_basedtax.taxonomy",
                              package = "CMETNGS",mustWork = TRUE)
edagraphs <- MakeEDABargraphs(shareddataset,taxonomydataset)

CMET-UGent/CMETNGS documentation built on Dec. 12, 2020, 8:22 a.m.