plot_pls: Plot PLSR

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

Plot PLSR

Description

Plot PLSR error and calibration / crossvalidation plots.

Usage

## S4 method for signature 'aquap_cube'
plot_pls(object, ...)

Arguments

object

An object of class 'aquap_cube' as produced by gdmm.

...

Optional 'pls' plotting parameters to override the values in the analysis procedure - for possible arguments see plot_pls_args and below: 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. rv.bandwidth Character "def", or numeric length one. The bandwidth of wavelengths used in the peak-picking process when plotting the regression vector. If left at the default "def", the value from the settings.r file (parameter pp_bandwidth) is used. rv.adLine Logical, numeric or character 'def'. If set to FALSE, no additional lines, if set to TRUE all the additional lines will be plotted in the loading plot. If an integer vector [2..5] is provided, one or more of the additional lines get plotted. See adLinesToVector for details. If left at the default value 'def', the value from the settings.r file (parameter plsr_AdLines) is used. rv.col Character "def" or a valid color. A possible custom color for coloring the plsr regression vector. When left at the default "def" the value fromt the settings.r file is read in (parameter plsr_rv_customColor). Provide a color-vector to use it for coloring the plsr regression vector. rv.lty Character "def" or a positive integer indicating the desired line type. When left at the default "def" the value from the settings.r file is read in (parameter plsr_rv_customLinetype). psd 'plot secondary data'; either character 'def' or logical. If secondary (i.e. calibration data) should be plotted as well. Leave at the default 'def' to take the value from the parameter plsr_plot_secondaryData in the settings file, or provide TRUE or FALSE. The alpha level for the secondary data can be set in parameter plsr_color_alpha_secondaryData in the settings file.

Details

By providing one or more of the ... arguments you can override the plotting values in the selected analysis procedure, see examples. The width and height of the resulting pdf can be set in the settings.

Value

A pdf or graphic device.

See Also

Other Plot functions: plot,aquap_cube,missing-method, 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_indepPred(), plot_rnf,aquap_cube-method, plot_simca,aquap_cube-method, plot_svm,aquap_cube-method

Other PLSR documentation: calc_pls_args, plot_pls_args, plot_pls_indepPred()

Examples

 ## Not run: 
 dataset <- gfd()
 cube <- gdmm(dataset)
 plot(cube)
 plot_pls(cube)
 plot_pls(cube, aps="foobar.r") # to get the plotting parameters 
 # from the file "foobar.r".
 plot_pls(cube, lv.col="red") # to have the regression vector in red
 plot(cube, what="pls", pg.where="", rv.col="red", rv.lty=2)
 plot(cube, pg.where="", rv.col="red", rv.lty=2) 
 plot(cube, pls.what="regression") # for plsr, only plot the regression vector

## End(Not run)

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