| plot_pls,aquap_cube-method | R Documentation |
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.
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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)
