abundance_plot: abundance_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

abundance_plot

Description

Plots abundance among samples and groups (sample_group) at specific taxonomic level.

Usage

abundance_plot(otu, taxa, sample, sample_group, rank)

Arguments

otu	a community count data matrix with samples in rows and OTUs/taxa in column,
taxa	a taxa information matrix. The rownames must match the OTU names (taxa_names) of the otu,
sample	a sample information data.frame. The rownames must match the sample names in the otu,
sample_group	the name of a column that containing the sample type/group,
rank	a taxonomic rank (Phylum or Class or Order or Family or Genus or Species),

Details

Plots abundance among samples and groups (sample_group) at specific taxonomic level.

Value

two subfigures containing abundance among samples and groups (sample_group) at specific taxonomic level.

Examples

 abundance_plot(otu, taxa, sample, sample_group, 'Genus')

lindan1128/coreMicrobiome documentation built on May 5, 2022, 8:24 p.m.