phylogeny_profile: Create a ggplot object of the phylogenic barplots from a...

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

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

Description

Inputs a phyloseq-class object and creates phylogenic barplots.

Usage

phylogeny_profile(phyloseq_obj, treatment = NULL, subset = NULL,
classification = NULL, merge = TRUE, relative_abundance = FALSE,
colors = 'default', grid = FALSE, 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.
merge	if FALSE, will show separation of individuals within each classification.
relative_abundance	If TRUE, transforms the abundance data into relative abundance by sample.
colors	Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors.
grid	Wraps the sub-plots into a grid pattern rather than side-by-side.
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

phylogeny_profile(soil_column, classification = 'Phylum',
treatment = c('Matrix', 'Treatment'), merge = TRUE,
relative_abundance = TRUE)

schuyler-smith/phyloschuyler documentation built on Aug. 16, 2024, 5:36 a.m.