Koren Bodysites Case Study

For background information on the mixMC or sPLS-DA methods, refer to the MixMC Method Page and sPLS-DA Method Page.

The R script used for all the analysis in this case study is available here.

More information on Plots

For a more in depth explanation of how to use and interpret the plots seen, refer to the following pages:

• plotIndiv() – Sample Plot
• plotLoadings() – Loading Plot
• plotVar() – Correlation Circle Plot
• cim() – Cluster Image Maps
• network() – Relevance Network Graph

References

1. Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C. and Ley, R.E., 2013. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol, 9(1), p.e1002863
2. Lê Cao KA, Costello ME, Lakis VA, Bartolo F, Chua XY, et al. (2016) MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities. PLOS ONE 11(8): e0160169
3. Lê Cao, K.-A., Boitard, S., Besse, P.: Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC bioinformatics 12(1), 253 (2011)
4. Rohart F, Gautier B, Singh A, Lê Cao K-A (2017). mixOmics: an R package for ‘omics feature selection and multiple data integration.