taxa_abundance_bars: Create a ggplot object of the abundance barplots from a...

In schuyler-smith/phylosmith: Functions to help analyze data as phyloseq objects

Create a ggplot object of the abundance barplots from a phyloseq object. Function from the phylosmith-package.

Description

Inputs a phyloseq-class object and creates barplots of taxa by treatment.

Usage

taxa_abundance_bars(phyloseq_obj, treatment = NULL, subset = NULL,
classification = NULL, transformation = "none", colors = "default",
wrap_by = NULL, 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 number 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.
classification	Column name as a string or number in the tax_table for the factor to use for node colors.
transformation	Transformation to be used on the data. "none", "mean", "median", "sd", "log", "log10"
colors	Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors.
wrap_by	Column name as a string or number in the phyloseq sample_data to facet the ggplot figure by.
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

ggplot-object

Examples

taxa_abundance_bars(
taxa_filter(soil_column, frequency = 0.8),
classification = 'Phylum', treatment = c('Matrix', 'Treatment'),
subset = 'Unamended', transformation = 'mean')

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