mixOmics: An R package for ‘omics feature selection and multiple data integration
Fig 3
Illustration of a single ‘omics analysis with mixOmics.
A) Unsupervised preliminary analysis with PCA, A1: PCA sample plot, A2: percentage of explained variance per component. B) Supervised analysis with PLS-DA, B1: PLS-DA sample plot with confidence ellipse plots, B2: classification performance per component (overall and BER) for three prediction distances using repeated stratified cross-validation (10×5-fold CV). C) Supervised analysis and feature selection with sparse PLS-DA, C1: sPLS-DA sample plot with confidence ellipse plots, C2: arrow plot representing each sample pointing towards its outcome category, see more details in Supporting Information S1 Text. C3: Clustered Image Map (Euclidean Distance, Complete linkage) where samples are represented in rows and selected features in columns (10, 300 and 30 genes selected on each component respectively), C4: ROC curve and AUC averaged using one-vs-all comparisons.