Description Usage Arguments Details Value Author(s) References See Also
Function for plotting PCA, PLS or OPLS model scores.
1 2 |
model |
PCA, PLS or OPLS model of the package MetaboMate. |
pc |
Specifies which model components should be plotted on abscissa and ordinate (see Details). |
an |
Colour and label specification (see Details). |
title |
Plot title. |
qc |
Row indices of QC samples. Can be left NA, however, if specified QC samples will be highlighted in the plot. |
legend |
Position of the plot legend, set to NA if legend should be outside of the plotting area. |
cv.scores |
Logical value (TRUE or FALSE) indicating if cross-validated scores should be plotted for the predictive component(s) (only for PLS and O-PLS). |
... |
Additional values passed on to |
Scores colouring is specified with the argument an
, which is a list of three elements. The first list element specifies the colour (class factor required for categorical variables), the second list element specifies a point labeling (class character or factor) and the third list element specifies point shape. The Hotelling's T2 ellipse is automatically included and calculated for the dimensions selected by the pc
argument.
This function returns a ggplot2 plot object.
Torben Kimhofer tkimhofer@gmail.com
Trygg J. and Wold, S. (2002) Orthogonal projections to latent structures (O-PLS). Journal of Chemometrics, 16.3, 119-128.
Hotelling, H. (1931) The generalization of Student’s ratio. Ann. Math. Stat., 2, 360-378.
pca
opls
PCA_MetaboMate-class
OPLS_MetaboMate-class
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