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Generate heatmap (version 2.6.0.0)

Input file of microbial relative abundances:

This file is typically obtained with merge_metaphlan_tables

Format for the output image:

Hierarchical clustering method:

Distance function for samples:

Distance function for microbes:

Width of heatmap cells:

Automatically set, this option should not be necessary unless for very large heatmaps

Height of heatmap cells:

Automatically set, this option should not be necessary unless for very large heatmaps

Minimum value to display:

Values around 0.001 are also reasonable

Maximum value to display:

Default is maximum value present, can be set e.g. to 100 to display the full scale

Taxonomic level to display:

Percentile to be used for ordering the microbes:

Number of most abundant microbes to display:

Height of the sample dendrogram:

Width of the sample dendrogram:

Height of the colormap:

Label font sizes:

Line width for the dendrograms:

Taxonomic level to display:

What it does

MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the user manual.

This tool generates heatmaps with hierarchical clustering of both samples and microbial clades. The script can also subsample the number of clades to display based on the their nth percentile abundance value in each sample