reshape_metaphlan2_result: reshape_metaphlan2_result

In yeguanhuav/visual16S: Visualization functions for 16S and Metagenomics analysis

Description

This is a function that reshape metaphlan2 result for generating phyloseq object.

Usage

reshape_metaphlan2_result(
  metaphlan2_merged,
  remove_archaea = FALSE,
  remove_viruses = FALSE,
  level = "Species",
  abundance_filtering = 0.01,
  rescale = FALSE
)

Arguments

metaphlan2_merged	Input a metaphlan2 merged result.
remove_archaea	Default is FALSE. If TRUE, remove Archea.
remove_viruses	Default is FALSE. If TRUE, remove Viruses.
level	Choose a taxonomy level to extract. The level name should be one of "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species". Default is "Species".
abundance_filtering	Set metaphlan results that lower than abundance_filtering to 0. Default is 0.01, metaphlan results are relative abundance.
rescale	Default is FALSE. If TRUE, rescale the metaphlan results after filtering.

Examples

reshape_metaphlan2_result(metaphlan2_merged, level = "Species")

yeguanhuav/visual16S documentation built on Feb. 19, 2022, 10:32 a.m.