manta

For a demo run, a network generated from oral samples of bats has been included.

This data was downloaded from QIITA: https://qiita.ucsd.edu/study/description/11815

Lutz, H. L., Jackson, E. W., Dick, C., Webala, P. W., Babyesiza, W. S., Peterhans, J. C. K., … & Gilbert, J. A. (2018). Associations between Afrotropical bats, parasites, and microbial symbionts. bioRxiv, 340109.

In this dataset, the authors took samples from a number of bats. For the network analysis, only fecal samples were included; samples with fewer than 500 counts were removed and rarefied to even depth, while taxa with a prevalence below 10% were removed as well. A Spearman correlation network was generated from this data for associations with a p-value below 0.05.

The dataset can be accessed by specifying demo as the input variable.

manta -i demo -o outputpath/demo

The network below is a Cytoscape visualization of the network produced by the above command. Nodes were coloured by phylum-level taxonomy, while border colours map to strong (black) or weak (purple) assignments. Node positions were calculated with a force-directed layout algorithm; for this layout, use the Edge-weighted Spring Embedded Layout directly available in Cytoscape and specify the edge weight as the input. You can download the style used in the pictures below here.