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Plot heatmap of OTU table (version 1.9.1.0)
Samples will be clustered within each category level using euclidean UPGMA
If both this and the sample mapping file are provided, the mapping file is ignored.
Without this option, all zeros will be set to a small value (default is 1/2 the smallest non-zero entry). Data will be translated to be non-negative after log transform, and num_otu_hits will be set to 0.
If --otu_tree is provided, this flag is ignored.
If --map_fname is provided, this flag is ignored.

What it does

This script visualizes an OTU table as a heatmap where each row corresponds to an OTU and each column corresponds to a sample. The higher the relative abundance of an OTU in a sample, the more intense the color at the corresponsing position in the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical clustering, and the samples (columns) will be presented in the order in which they appear in the OTU table. Alternatively, the user may supply a tree to sort the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping file for sorting samples. If the user passes in a mapping file and a metadata category, samples (columns) will be grouped by category value and subsequently clustered within each group.

A single output file is created containing the heatmap of the OTU table (a PDF file by default).