plotRSDs() - Visualise the analytical and biological variance in Discretely sampled datasets.

plotScree() - Plot a barchart of variance explained (R2) and predicted (Q2) (if available) for each PCA component derived from a PCA model generated on Dataset datasets.

plotScores() - Plot PCA scores for each pair of components in PCAmodel, coloured by values defined in classes, and with Hotelling’s T2 ellipse (95%), derived from a PCA model generated on Dataset datasets.

plotOutliers() - Plot scatter plot of PCA outlier stats sumT (strong) or DmodX (moderate), with a line at [25, 50, 75, 95, 99] quantiles, derived from a PCA model generated on Dataset datasets.

plotLoadings() - Plot PCA loadings for each component in PCAmodel. For NMRDataset datasets plots the median spectrum coloured by the loading. For MSDataset datasets plots an ion map (rt vs. mz) coloured by the loading.

plotScoresInteractive() - Interactively visualise PCA scores (coloured by a given sampleMetadata field, and for a given pair of components) with plotly, provides tooltips to allow identification of samples, derived from a PCA model generated on Dataset datasets.

plotLoadingsInteractive() - Interactively visualise PCA loadings (for a given pair of components) with plotly, provides tooltips to allow identification of features., derived from a PCA model generated on Dataset datasets.