plot_aqg_args: Plot Aquagram - Arguments

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

Plot Aquagram - Arguments

Description

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

plot(cube, ...)

plot_aqg(cube, ...)

Arguments

do.aqg	Logical. If used in a plotting function, if Aquagrams should be plotted.
aqg.fsa	'Fix scale for Aquagram'. Logical, numeric or Character. If left at the default logical FALSE, every single aquagram will be plotted in its own, independent scale. If a numeric vector length two is provided, all the aquagrams to be plotted (normal AND bootstrapped ones) will be in the provided range, no independently scaled aquagrams will be plotted. If character, the following values are possible: "both": both independently scaled AND automatically calculated fix-scaled aquagrams will be plotted "only": only the automatically calculated fix-scaled aquagrams will be plotted. (normal AND bootstrap)
aqg.fss	'Fix scale for subtraction spectra'. Logical, numeric or character. If left at the default logical FALSE', every single subtraction-spectra plot will be plotted in its own, independendent scale. If a numeric vector length two is provided, all the subtraction-spectra to be plotted (if 'plotSpectra' contains 'subtr', and 'minus' contains a valid value) will be in the provided range, no independently scaled subtraction-spectra will be plotted. If character, the following values are possible: "both": both independently scaled AND automatically calculated fix-scaled spectra will be plotted "only": only the automatically calulated fix-scaled subtraction spectra will be plotted
aqg.ccol	Custom Color - NULL, Numeric or Character vector. Custom colors for drawing the lines in the aquagram. Length must exactly match the number of groups to be plotted in the aquagram. If not, the default coloring from the dataset is used. This can be used when plotting aquagrams with different numbers of groups: only this group that matches the number of provided custom colors is colored differently. Especially useful when you have more than 8 lines to be plotted – custom-color similar groups in similar colors.
aqg.clt	Character or Integer vector. Custom line type for plotting the lines in the Aquagram. If left at the default 'def', the vector provided in the settings.r file is taken (and recycled). If an integer vector is provided, this is used (and recycled) as line-types in the Aquagram.
aqg.pplot	Logical or character 'def'. If, should spectra be plotted, an additional plot with picked peaks should be added. If left at the default value 'def', the default from the settings.r file is used.
aqg.plines	Logical, numeric or character 'def'. If set to FALSE, no additional lines, if set to TRUE all the additional lines will be plotted. 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 default from the settings.r file (parameter aqg_AdLines) is used.
aqg.discr	Logical or character 'def'. If set to TRUE, negative (resp. positive) peaks can be only found in peak-heights below (resp. above) zero.
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_aqg

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

Other Aquagram documentation: calc_aqg_args, plot_aqg(), tempCalib_procedures

Examples

## Not run: 
dataset <- gfd()
cube <- gdmm(dataset)
plot(cube)

## End(Not run)

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