Microbiome.Heatmap: Microbiome.Heatmap.R

In jbisanz/MicrobeR: Handy functions for microbiome analysis in R

Description

Creates a heat map based based on user provided table. Transforms to log2(percent), log10(percent), or CLR as requested. For plotting purposes, a prior of 0.01

Usage

Microbiome.Heatmap(FEATURES, METADATA, NTOPFEATURES, TRANSFORM, CATEGORY,
  ROWCLUSTER)

Arguments

FEATURES	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names.
METADATA	Metadata file to be used for blocking.
NTOPFEATURES	The N most abundance features to plot (defaults to all). Calculated by taking largest row sums of percentage data
TRANSFORM	Method to transform data with for plotting, valid options are log2, log10, clr, percent, zscore or none (defaults to log10). None would be ideal if for example a list of fold changes was supplied. Zscore is calculated on clr.
CATEGORY	(optional) Category to create separate blocks (default: order of samples in otutable)
ROWCLUSTER	(optional) How to order rows. Valid options are: UPGMA or abundance, default is UPGMA which is UPGMA clustering of euclidean distance of CLR-normalized counts

Value

Prints a ggplot2 heatmap

jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.