dendrogram_phyloseq: Create a ggplot object of the dendrogram from a phyloseq...

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

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

Description

Inputs a phyloseq-class object and plots the dendrogram of samples colored by treatment.

Usage

dendrogram_phyloseq(phyloseq_obj, treatment, method = 'bray',
colors = 'default')

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.
method	the distance measurement algorithm to use, match to "euclidean", "manhattan", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao" or "mahalanobis".
colors	Name of a color set from the RColorBrewer package or a vector palette of R-accepted colors.

Value

ggplot-object

Examples

dendrogram_phyloseq(soil_column, c('Matrix', 'Treatment'))

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