abundance_heatmap: Create a heatmap of the out_table from a phyloseq-object.

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

Create a heatmap of the out_table from a phyloseq-object.

Description

Uses a phyloseq-class object as input and creates a ggplot-heatmap of the abundances across samples. The default color choice is the viridis palette.

Usage

abundance_heatmap(phyloseq_obj, classification = NULL, 
  treatment =  NULL, subset = NULL, transformation = 'none', 
  colors = 'default', treatment_labels = NULL, sample_labels = NULL,
  classification_labels= NULL)

Arguments

phyloseq_obj	A phyloseq-class object.
classification	The level of taxonomy to examine. Must be a column name from the tax_table of the phyloseq_object. tax_table.
treatment	Column name as a string, or vector of strings, from the sample_data.
subset	A level within the treatment. Multiple levels can be given as a vector.
transformation	Transformation to be used on the data. "none", "relative_abundance", "log", "log10", "log1p", "log2", "asn", "atanh", "boxcox", "exp", "identity", "logit", "probability", "probit", "reciprocal", "reverse" and "sqrt"
colors	Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors. The default is an adaption of the palette from https://www.nature.com/articles/nmeth.1618
treatment_labels	a vector of names to be used as labels for treatments/facets, in the order they appear in the figure.
sample_labels	a vector of names to be used as labels for Samples, in the order they appear in the figure.
classification_labels	a vector of names to be used as labels for the taxonomic classifications, in the order they appear in the figure.

Value

ggplot-object

Examples

data(GlobalPatterns)
abundance_heatmap(GlobalPatterns, classification = "Phylum",
 treatment = "SampleType", transformation = "log2")

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