taxa_heatmap: taxa_heatmap

In jbisanz/qiime2R: qiime2R

taxa_heatmap

Description

Uses ggplot2 to create a heatmap, for example on phylum level abundances. The most abundant features (defaults to 10, based on rowMeans) will be plotted unless user specified.

Usage

taxa_heatmap(features, metadata, "treatment")

Arguments

features	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names
metadata	A Table of metadata where sample names are the row names OR there is already a column with the name "SampleID"
category	A metadata category to block samples by which is a column in the metadata (faceting via ggplot2)
normalize	How should table be normalized? default="log10(percent)", options=c("log10(percent)","clr","none"). Note if using log10(percent), a pseudocount 1 read is added before conversion to percent
ntoplot	A number of features to plot.

Value

Barplot

jbisanz/qiime2R documentation built on April 24, 2024, 5 p.m.