plot_pca_args: Plot PCA - Arguments

In bpollner/aquap2: Multivariate Data Analysis Tools for R including Aquaphotomics Methods

Plot PCA - Arguments

Description

The following parameters can be used in the ... argument in function plot and plot_pca to override the values in the analysis procedure file and so to modify the graphics of score and loading plots - see examples.

plot(cube, ...)

plot_pca(cube, ...)

plot_pca(dataset, ...)

Arguments

do.pca	Logical. If used in a plotting function, if PCA score / loading plots should be plotted.
pca.colorBy	NULL or character vector. Which class-variables should be used for coloring the PCA score plot. Set to NULL for using all available class variables for coloring.
pca.elci	'def' or numeric length one. The confidence interval for the ellipse to be drawn around groups in score plots. Leave at 'def' to read in the default from the settings.r file; provide a numeric length one (e.g. 0.95); or set to NULL for not drawing ellipses at all.
pca.elcolorBy	Character vector or NULL. The variables to use for plotting additional confidence intervall ellipses. Set to NULL for *not* drawing additional CI-ellipses. Provide one variable (gets recycled) or a vector with equal length as pca.colorBy to have the additional CI-ellipses along these variables.
pca.what	Character length one. What element of the PCA analysis to plot. Possible values are 'both', 'scores', 'loadings'.
pca.sc	Numeric length 2. Two PCs to be plotted against each other in the score plots.
pca.sc.pairs	Numeric vector of length >=2, indicating what PCs to plot in the score pairs plot. Set to NULL for *not* plotting the pairs plot.
pca.lo	Numeric vector of length >=2, indicating what PCs to plot in the loadingplot.
pg.where	Character length one. If left at the default 'def', the value from the settings.r file is read in (parameter gen_plot_pgWhereDefault). For plotting to PDFs provide "pdf", for plotting to graphics device provide anything but "pdf".
pg.main	Character length one. The additional text on the title of each single plot.
pg.sub	Character length one. The additional text on the subtitle of each single plot.
pg.fns	Character length one. The additional text in the filename of the pdf.

Details

For a list of all parameters that can be used in the ... argument in getap and in the plot functions please see anproc_file.

See Also

plot_pca

Other Plot arguments: plot,aquap_data,missing-method, plot_NNET_args, plot_SVM_args, plot_aqg_args, plot_discrimAnalysis_args, plot_pg_args, plot_pls_args, plot_randomForest_args, plot_sim_args

Other PCA documentation: calc_pca_args, plot_pca,aquap_cube-method

Examples

## Not run: 
dataset <- gfd()
cube <- gdmm(dataset)
plot(cube, pca.colorBy="C_Group", pca.sc.pairs=NULL) 
# will plot every available model
plot_pca(cube, pca.colorBy="C_Group", pca.sc.pairs=NULL) 
# will plot only the PCA
plot_pca(cube, pca.what="scores")

## End(Not run)

bpollner/aquap2 documentation built on March 29, 2024, 7:33 a.m.