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Plot function for an RLum.Data.Spectrum S4 class object

Source: R/plot_RLum.Data.Spectrum.R
plot_RLum.Data.Spectrum.Rd

The function provides a standardised plot output for spectrum data of an RLum.Data.Spectrum class object. The purpose of this function is to provide easy and straight-forward spectra plotting, not provide a full customised access to all plot parameters. If this is wanted, standard R plot functionality should be used instead.

Matrix structure
(cf. RLum.Data.Spectrum)

  • rows (x-values): wavelengths/channels (xlim, xlab)

  • columns (y-values): time/temperature (ylim, ylab)

  • cells (z-values): count values (zlim, zlab)

Note: This nomenclature is valid for all plot types of this function!

Nomenclature for value limiting

  • xlim: Limits values along the wavelength axis

  • ylim: Limits values along the time/temperature axis

  • zlim: Limits values along the count value axis

Details on the plot functions

Spectrum is visualised as 3D or 2D plot. Both plot types are based on internal R plot functions.

plot.type = "persp"

Arguments that will be passed to graphics::persp:

  • shade: default is 0.4

  • phi: default is 15

  • theta: default is -30

  • lphi: default is 15

  • ltheta: default is -30

  • expand: default is 1

  • axes: default is TRUE

  • box: default is TRUE; accepts "alternate" for a custom plot design

  • ticktype: default is detailed, r: default is 10

Note: Further parameters can be adjusted via par. For example to set the background transparent and reduce the thickness of the lines use: par(bg = NA, lwd = 0.7) previous the function call.

plot.type = "single"

Per frame a single curve is returned. Frames are time or temperature steps.

-frames: pick the frames to be plotted (depends on the binning!). Check without this setting before plotting.

plot.type = "multiple.lines"

All frames plotted in one frame.

-frames: pick the frames to be plotted (depends on the binning!). Check without this setting before plotting.

plot.type = "image" or plot.type = "contour"

These plot types use the R functions graphics::image or graphics::contour. The advantage is that many plots can be arranged conveniently using standard R plot functionality. If plot.type = "image" a contour is added by default, which can be disabled using the argument contour = FALSE to add own contour lines of choice.

plot.type = "transect"

Depending on the selected wavelength/channel range a transect over the time/temperature (y-axis) will be plotted along the wavelength/channels (x-axis). If the range contains more than one channel, values (z-values) are summed up. To select a transect use the xlim argument, e.g. xlim = c(300,310) plot along the summed up count values of channel 300 to 310.

Further arguments that will be passed (depending on the plot type)

xlab, ylab, zlab, xlim, ylim, box, zlim, main, mtext, pch, type ("single", "multiple.lines", "interactive"), col, border, lwd, bty, showscale ("interactive", "image") contour, contour.col ("image")

Usage

plot_RLum.Data.Spectrum(
  object,
  par.local = TRUE,
  plot.type = "contour",
  optical.wavelength.colours = TRUE,
  bg.spectrum = NULL,
  bg.channels = NULL,
  bin.rows = 1,
  bin.cols = 1,
  norm = NULL,
  rug = TRUE,
  limit_counts = NULL,
  xaxis.energy = FALSE,
  legend.text,
  plot = TRUE,
  ...
)

Arguments

object

RLum.Data.Spectrum or matrix (required): S4 object of class RLum.Data.Spectrum or a matrix containing count values of the spectrum.
Please note that in case of a matrix row names and col names are set automatically if not provided.

par.local

logical (with default): use local graphical parameters for plotting, e.g. the plot is shown in one column and one row. If par.local = FALSE global parameters are inherited.

plot.type

character (with default): plot type, for 3D-plot use persp, or interactive, for a 2D-plot image, contour, single or multiple.lines (along the time or temperature axis) or transect (along the wavelength axis)

optical.wavelength.colours

logical (with default): use optical wavelength colour palette. Note: For this, the spectrum range is limited: c(350,750). Own colours can be set with the argument col. If you provide already binned spectra, the colour assignment is likely to be wrong, since the colour gradients are calculated using the bin number.

bg.spectrum

RLum.Data.Spectrum or matrix (optional): Spectrum used for the background subtraction. By definition, the background spectrum should have been measured with the same setting as the signal spectrum. If a spectrum is provided, the argument bg.channels works only on the provided background spectrum.

bg.channels

vector (optional): defines channel for background subtraction If a vector is provided the mean of the channels is used for subtraction. If a spectrum is provided via bg.spectrum, this argument only works on the bg.spectrum.

Note: Background subtraction is applied prior to channel binning

bin.rows

integer (with default): allow summing-up wavelength channels (horizontal binning), e.g. bin.rows = 2 two channels are summed up. Binning is applied after the background subtraction.

bin.cols

integer (with default): allow summing-up channel counts (vertical binning) for plotting, e.g. bin.cols = 2 two channels are summed up. Binning is applied after the background subtraction.

norm

character (optional): Normalise data to the maximum (norm = "max") or minimum (norm = "min") count values. The normalisation is applied after the binning.

rug

logical (with default): enables or disables colour rug. Currently only implemented for plot type multiple.lines and single

limit_counts

numeric (optional): value to limit all count values to this value, i.e. all count values above this threshold will be replaced by this threshold. This is helpful especially in case of TL-spectra.

xaxis.energy

logical (with default): enables or disables energy instead of wavelength axis. For the conversion the function convert_Wavelength2Energy is used.

Note: This option means not only simply redrawing the axis, instead the spectrum in terms of intensity is recalculated, s. details.

legend.text

character (with default): possibility to provide own legend text. This argument is only considered for plot types providing a legend, e.g. plot.type="transect"

plot

logical (with default): enables/disables plot output. If the plot output is disabled, the matrix used for the plotting and the calculated colour values (as attributes) are returned. This way, the (binned, transformed etc.) output can be used in other functions and packages, such as plotting with the package 'plot3D'

...

further arguments and graphical parameters that will be passed to the plot function.

Value

Returns a plot and the transformed matrix used for plotting with some useful attributes such as the colour and pmat (the transpose matrix from graphics::persp)

Note

Not all additional arguments (...) will be passed similarly!

Function version

0.6.9

See also

RLum.Data.Spectrum, convert_Wavelength2Energy, plot, plot_RLum, graphics::persp, plotly::plot_ly, graphics::contour, graphics::image

Author

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

How to cite

Kreutzer, S., 2024. plot_RLum.Data.Spectrum(): Plot function for an RLum.Data.Spectrum S4 class object. Function version 0.6.9. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.26. https://r-lum.github.io/Luminescence/

Examples


##load example data
data(ExampleData.XSYG, envir = environment())

##(1)plot simple spectrum (2D) - image
plot_RLum.Data.Spectrum(
 TL.Spectrum,
 plot.type="image",
 xlim = c(310,750),
 ylim = c(0,300),
 bin.rows=10,
 bin.cols = 1)
#> Warning: [plot_RLum.Data.Spectrum()] 6 channels removed due to row (wavelength) binning


##(2) plot spectrum (3D)
plot_RLum.Data.Spectrum(
  TL.Spectrum,
  plot.type="persp",
  xlim = c(310,750),
  ylim = c(0,100),
  bin.rows=10,
  bin.cols = 1)
#> Warning: [plot_RLum.Data.Spectrum()] 6 channels removed due to row (wavelength) binning


##(3) plot spectrum on energy axis
##please note the background subtraction
plot_RLum.Data.Spectrum(TL.Spectrum,
plot.type="persp",
ylim = c(0,200),
bin.rows=10,
bg.channels = 10,
bin.cols = 1,
xaxis.energy = TRUE)
#> Warning: [plot_RLum.Data.Spectrum()] 3 channels removed due to row (wavelength) binning


##(4) plot multiple lines (2D) - multiple.lines (with ylim)
plot_RLum.Data.Spectrum(
 TL.Spectrum,
 plot.type="multiple.lines",
 xlim = c(310,750),
 ylim = c(0,100),
 bin.rows=10,
 bin.cols = 1)
#> Warning: [plot_RLum.Data.Spectrum()] 6 channels removed due to row (wavelength) binning


if (FALSE) { # \dontrun{
 ##(4) interactive plot using the package plotly ("surface")
 plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive",
 xlim = c(310,750), ylim = c(0,300), bin.rows=10,
 bin.cols = 1)

 ##(5) interactive plot using the package plotly ("contour")
 plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive",
 xlim = c(310,750), ylim = c(0,300), bin.rows=10,
 bin.cols = 1,
 type = "contour",
 showscale = TRUE)

 ##(6) interactive plot using the package plotly ("heatmap")
 plot_RLum.Data.Spectrum(TL.Spectrum, plot.type="interactive",
 xlim = c(310,750), ylim = c(0,300), bin.rows=10,
 bin.cols = 1,
 type = "heatmap",
 showscale = TRUE)

} # }