taxa_core_graph: Create graph of the core taxa seen in phyloseq-object over a...

View source: R/taxa_core_graph.R

taxa_core_graphR 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.

Value

phyloseq-object

Examples

taxa_core_graph(soil_column)

schuyler-smith/phylosmith documentation built on Aug. 17, 2024, 10:19 a.m.