A recent paper by Coutinho et al. (Nature Comm. 2017) claims to find evidence to support the Piggyback-the-Winner hypothesis that lysogeny prevalence increases at high microbial abundances. In [2], we find absence of evidence for positive correlations between virus and microbial abundances. This repository contains the codes used to support our response to the findings of Coutinho et al.

This repository contains codes for

• Recreating the subplots reported in [1] (folder: figures/host-vhr), and
• Creating the figures used for our analysis (folders: figures/host-virus and rendomization_test).

Each folder includes two codes: one for the genus datasets and one for the phylum datasets. All codes are in Python version 2.7.

This code is archived on Zenodo:

References

[1] Coutinho, F. H., Silveira, C. B., Gregoracci, G. B., Thompson, C. C., Edwards, R. A., Brussaard, C. P. D., Dutilh, B. E. & Thompson, F. L. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nature Communications 8, 15955 EP (2017).

[2] Al-Rasheed H., Jin R., & Weitz J. S. Caution in inferring viral strategies from abundance-based correlations in marine metagenomes (submitted).