plot_simca: Plot SIMCA

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

Plot SIMCA

Description

Plot SIMCA interclass distances.

Usage

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

Arguments

object

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

...

Optional 'simca' plotting parameters to override the values in the analysis procedure - for possible arguments see plot_sim_args and here 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. sim.distType The type of distance to be calculated, can be either 'od' or 'sd'. Defaults to 'od', the standardized orthogonal distances (see PredictSimca-class in package 'rrcovHD') sim.icdRan Can be 'def', NULL, or a numeric length one. The range for all the interclass-distance barplots. Set to NULL for no pre-defined range at all, or provide a numeric length one to specify the upper limit on the Y-axis of the interclass distances to be plotted. If values higher than specified appear, the range will be extended automatically. If left at the default 'def', the value from the settings.r file (parameter simca_rangeForDistBarPlots) is read in.

Details

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,aquap_cube-method, plot_pls_indepPred(), plot_rnf,aquap_cube-method, plot_svm,aquap_cube-method

Other SIMCA documentation: calc_sim_args, plot_sim_args

Examples

 ## Not run: 
 dataset <- gfd()
 cube <- gdmm(dataset)
 plot(cube)
 plot_simca(cube)
 plot(cube, what="sim", aps="foo.r") # take the analysis procedure from the 
 # file 'foo.r'
 plot_simca(cube, aps="cube", pg.main="FooBar") # Take the plotting parameter 
 from the cube itself, and add 'FooBar' to the main of every graphic.
 plot_simca(cube, aps="cube", pg.main="FooBar", pg.where="pdf") # same as 
 # above, but have the graphics in a PDF.
 plot_simca(cube, pg.main="Foo", pg.fns="_foo") # use the default for aps, 
 # add 'Foo' on each main, and add '_foo' to the filename of the possible pdf
 plot_simca(cube, sim.icdRan=2)
 plot(cube, sim.icdRan=2)
 plot_simca(cube, sim.icdRan=NULL) # to not have a pre-defined range

## End(Not run)

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