ABSTRACT
The mixOmics package places a strong emphasis on graphical visualisation for biological interpretation. Each analytical method in mixOmics is paired with insightful and user-friendly graphical outputs to facilitate understanding of the relationships between omics samples, associations or correlations between different biological variables. These plots are especially relevant when data sets contain information from different biological sources.
This chapter describes the various visualisation options available in the mixOmics package, and how they are structured to offer insights into the component scores (e.g. sample plots), loading vectors (e.g. variable plots such as correlation circle plots, loading plots, relevance networks and clustered image maps) or both (e.g. biplots) that result from PLS methods. All mixOmics plot options are consistent in their parameters and outputs across different methods to facilitate a user-friendly visualisation of the data.
