plot_all_modells: *** Plot All Available Models ***

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

*** Plot All Available Models ***

Description

Plot all available analysis graphics from the models in the cube-object. Function plot is a convenience function, it basically calls plot_cube, what is the work-horse for plotting the cube-object.

Usage

## S4 method for signature 'aquap_cube,missing'
plot(x, y, ...)

plot_cube(x, what = "all", ...)

Arguments

x	An object of class 'aquap_cube' as produced by gdmm.
y	will be ignored
...	Additional parameters to override the values of the graphical parameters in the analysis procedure and to override the defaults of the arguments in the underlying plotting functions like e.g. plot_pca. Plase see details and the documentation for the other plot functions. To specify the source of the analysis procedure and so of the plottig parameters use the argument aps Character length one. The default way to obtain the analysis procedure. Defaults to "def". Possible values are: "def" The default from the settings.r file is taken. (Argument gen_plot_anprocSource) "cube" Take the analysis procedure from within the cube, i.e. the analysis procedure that was used when creating the cube via gdmm is used. "defFile" Use the analysis procedure with the default filename as specified in the settings.r file in fn_anProcDefFile. Custom filename Provide any valid filename for an analysis procedure to use as input for specifying the plotting options.
what	Character length one. What type of analysis to plot. Possible values are 'all', 'pca', 'sim', 'pls', 'aqg', 'da', 'rnf', 'svm', 'nnet'.

Details

The graphical parameters for plotting are obtained either from the standard analysis procedure file, from a custom analysis procedure file, or from the analysis procedure embedded in the cube when it was generated via gdmm. To specify the source of the analysis procedure and so of the plottig parameters use the argument aps in the ... argument; the default for aps is "def", meaning that the default value as stored in the settings.r file (parameter gen_plot_anprocSource) is obtained. Generally, via the ... argument it is possible to override any of the plotting parameters. Please see anproc_file for a complete listing and e.g. plot_pca_args and there the other functions of the 'Plot arguments' family for a separate listing of possible arguments. Consult the documentation for the other plot functions like e.g. plot_pca for the arguments in the underlying plot functions not contained in the analysis procedure – see examples.

Value

A PDF or graphic device.

See Also

plot_spectra

Other Core functions: exportSampleList(), gdmm(), getFullData(), plot,aquap_data,missing-method

Other Plot functions: plot,aquap_data,missing-method, plot_aqg(), plot_classifX_indepPred(), plot_da,aquap_cube-method, plot_nnet,aquap_cube-method, plot_pca,aquap_cube-method, plot_pls,aquap_cube-method, plot_pls_indepPred(), plot_rnf,aquap_cube-method, plot_simca,aquap_cube-method, plot_svm,aquap_cube-method

Examples

## Not run: 
 dataset <- gfd()
 cube <- gdmm(dataset)
 plot(cube)
 plot(cube, what="all") # the same as above
 plot(cube, what="pca")
 plot(cube, what="pca", pg.main="FooBar") # add "FooBar" to main
 plot(cube, what="pca", aps="foo.r", ld.col=c("green", "blue")) # to load the
 # analysis procedure from a file called "foo.r", and to have the loadings in 
 # the pca drawn in green and blue.

## End(Not run)

bpollner/aquap2 documentation built on June 29, 2024, 5:21 p.m.