The academic dashboard is built for in-depth exploration of metagenomic datasets. It lets you analyse the structure of microbial communities and identify the environmental factors driving how they assemble.
6 sections · about 10 min read
Before comparing samples against each other, it's worth defining what is measured within a single sample. Alpha diversity assesses richness — the number of variants or OTUs/ASVs — and evenness, that is, how their abundances are distributed, within one local environment.
Before projecting whole communities, you often need to understand how the metadata interact with one another and with the microbiome's global indices. The interface offers two levels of analysis.
Beta diversity measures the distance — the compositional dissimilarity — between different samples. Where alpha diversity describes a sample in isolation, beta diversity describes what separates two samples.
The interface offers a view of the composition of the three taxa under study through UMAP (Uniform Manifold Approximation and Projection), a non-linear dimensionality reduction technique. It projects the complexity of each sample's relative abundance profile onto two dimensions (UMAP 1 and UMAP 2), preserving the local and global topological structure of the data better than a classical PCoA.
The tool lets you overlay continuous metadata onto the UMAP projection to visually assess the effect of a gradient — pH, sand percentage, carbon percentage — on microbial composition.
The application generates three independent visualization panes at once, so you can compare how the different kingdoms respond ecologically to the same gradient.