taxa_core_graph: Create graph of the core taxa seen in phyloseq-object over a...
In schuyler-smith/phylosmith: Functions to help analyze data as phyloseq objects

taxa_core_graph

R Documentation

Create graph of the core taxa seen in phyloseq-object over a range of abundance and smaple-frequency values. Function from the phylosmith-package.

Description

Inputs a phyloseq object and finds which taxa are seen in a given proportion of samples at a minimum relative abundance, either in the entire dataset, or by treatment, over a range of values. Then draws the distribution.

Usage

taxa_core_graph(phyloseq_obj, treatment = NULL, subset = NULL,
frequencies = seq(0.1, 1, 0.1), abundance_thresholds = seq(0.01, 1, 0.01),
colors = 'default',
treatment_labels = NULL, sample_labels = NULL, classification_labels= NULL)

Arguments

`phyloseq_obj`	A `phyloseq-class` object. It must contain `sample_data()`) with information about each sample, and it must contain `tax_table()`) with information about each taxa/gene.
`treatment`	Column name as a `string` or `numeric` in the `sample_data`. This can be a vector of multiple columns and they will be combined into a new column.
`subset`	A factor within the `treatment`. This will remove any samples that to not contain this factor. This can be a vector of multiple factors to subset on.
`frequencies`	The range of proportions of samples the taxa are found in.
`abundance_thresholds`	The range of minimum relative abundances the taxa are found in for each sample.
`colors`	Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors.
`treatment_labels`	a vector of names to be used as labels for treatments/facets.
`sample_labels`	a vector of names to be used as labels for Samples.
`classification_labels`	a vector of names to be used as labels for the taxonomic classifications.