module_env_correlation: Relationship between sub-communities and environment

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

Description

This function calculates correlation between modules (sub-communities) and environmental variables. The most connected node(taxon) in a given module is considered a good representation of the module. This is implemented in accordance to (Deng et al. 2012) where correlations between module-based eigengenes and environmental factors are used to detect the modules' response to environmental change.

Usage

module_env_correlation(co_occur_res, select.variables = NULL, ...)

Arguments

co_occur_res	an object returned by 'co_occurence_network' function.
select.variables	environmental variables of interest.

Author(s)

Alfred Ssekagiri [e-mail], Umer Zeeshan Ijaz [e-mail]

References

http://userweb.eng.gla.ac.uk/umer.ijaz/, Umer Ijaz, 2015

Deng, Ye, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, and Jizhong Zhou. 2012. “Molecular Ecological Network Analyses.” BMC Bioinformatics 13 (1). BioMed Central: 113.

Examples

mod.env.cor <- module_env_correlation(co_occur)
p <- plot_taxa_env(mod.env.cor)
print(p)

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.