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A Comparison of the Experimental and Simulated Forms of EPR Spectra

Source: R/present_EPR_Sim_Spec.R
present_EPR_Sim_Spec.Rd

Presenting experimental as well as simulated/fitted EPR spectra together in one ggplot2 object. They are visualized in two possible modes. Despite the fact that quite often two spectra are compared in overlay mode, sometimes it is rather difficult to figure out differences between the experimental and the simulated EPR spectrum by such manner (the details can be "hidden" in overlays). Therefore, there is also an option to offset the EPR simulated spectrum underneath the experimental one, see argument Intensity.shift.ratio. For the sake of presentation, the maximum-minimum intensity difference, of the simulated spectrum, is automatically scaled onto the experimental one.

Usage

present_EPR_Sim_Spec(
  data.spectr.expr,
  data.spectr.sim,
  B.unit = "G",
  Blim = NULL,
  Intensity.expr = "dIepr_over_dB",
  Intensity.sim = "dIeprSim_over_dB",
  Intensity.shift.ratio = 1.2,
  B.shift = 0,
  lineSpecs.form = "derivative",
  line.color.expr = "red",
  line.color.sim = "blue",
  line.width = 0.75,
  output.df = FALSE
)

Arguments

data.spectr.expr

Data frame object related to experimental spectrum, including the magnetic flux density (in mT or G) column, which can be labeled as B_mT in mT (or B_G in gauss), and the intensity column such as dIepr_over_dB, where the index column can be included as well.

data.spectr.sim

Data frame object related to experimental spectrum including the magnetic flux density (in mT or G) column, which can be labeled as Bsim_mT in mT (or Bsim_G in gauss), and the intensity column such as dIeprSim_over_dB. These column names are acquired automatically if function like the readEPR_Sim_Spec or the eval_sim_EPR_iso is used to get the simulated spectrum data in ASCII.

B.unit

Character string, pointing to unit of magnetic flux density (coming from the original datasets) which is to be presented on \(B\)-axis of the EPR spectrum. Strings like "G" (`Gauss`) (default) or "mT" (`millitesla`) can be used.

Blim

Numeric vector, magnetic flux density in mT/G corresponding to lower and upper visual limit of the selected \(B\)-region, such as Blim = c(3495.4,3595.4). Default: Blim = NULL (corresponding to the entire \(B\)-range of both EPR spectra).

Intensity.expr

Character string, referring to intensity column name if other than dIepr_over_dB name/label is used (e.g. for integrated spectra), default: Intesity = "dIepr_over_dB".

Intensity.sim

Character string, referring to intensity column name of the simulated spectrum if other than dIeprSim_over_dB name/label is used (e.g. for integrated spectra), default: Intesity = "dIeprSim_over_dB", which is automatically set if the readEPR_Sim_Spec function is used to read the spectrum in ASCII.

Intensity.shift.ratio

Numeric (CANNOT BE 0), showing how 'far' is the simulated EPR spectrum presented underneath the experimental one. The lower the ratio, the 'deeper' the simulated spectrum offset, default: Intensity.shift.ratio = 1.2, other common values : 0.6,0.8, 1.2,1.1. If the Intensity.shift.ratio = NULL, BOTH SPECTRA ARE PRESENTED IN OVERLAY MODE !

B.shift

Numeric, difference between the \(B_{center}\) of simulated and experimental spectrum, that can be caused by switching ON the Teslameter. It refers to simulated spectrum, default: B.shift = 0 (NOTE: It depends on the B parameter. If B.unit = "mT" => B.shift must be in mT, or if B.unit = "G" then B.shift must be in G).

lineSpecs.form

Character string, describing either "derivative" (default) or "integrated" (i.e. "absorption" or sigmoid-integrated, which can be used as well) line form of the analyzed EPR spectrum/data.

line.color.expr

Character string, line color to plot simple EPR spectrum. All ggplot2 compatible colors are allowed (see also plot_EPR_Specs), default: line.color = "red", should be different from line.color.sim.

line.color.sim

Character string, line color to plot simple EPR spectrum. All ggplot2 compatible colors are allowed, default: line.color = "blue", should be different from line.color.expr.

line.width

Numeric, linewidth of the plot line in mm, default: line.width = 0.75.

output.df

Logical, whether the data frame, corresponding to graphic spectra comparison (this actually corresponds to merging of the above-mentioned data frames by dplyr::bind_cols) should be returned as well (output.df = TRUE). In such case, the output is list containing plot (list$plot) as well as the data frame (list$df). However, the default is output.df = FALSE, i.e. only graphical representation is shown.

Value

Plot object (list) of the experimental and the simulated EPR (in derivative or integrated form) spectrum or list consisting of plot and the corresponding data frame df. Any output plot corresponds to simple ggplot2 object and can be combined with a desired theme (e.g. with plot_theme_NoY_ticks, see also Examples).

See also

Other Visualizations and Graphics: draw_molecule_by_rcdk(), plot_EPR_Specs(), plot_EPR_Specs2D_interact(), plot_EPR_Specs3D_interact(), plot_EPR_Specs_integ(), plot_EPR_present_interact(), plot_labels_xyz(), plot_layout2D_interact(), plot_theme_In_ticks(), plot_theme_NoY_ticks(), plot_theme_Out_ticks()

Examples

## load package built-in EPR spectral
## data example:
data.file.path <-
  load_data_example(file =
    "TMPD_specelchem_accu_b.asc")
data.spectrum.expr <-
  readEPR_Exp_Specs(path_to_ASC =
             data.file.path,
    col.names = c("B_G",
    "dIepr_over_dB"),
    qValue = 3500,
    origin = "winepr"
   )
#
## instrumental parameters for the spectrum,
## by the `WinEPR` spectrometer software
tmpd.params.file <-
  load_data_example(file =
    "TMPD_specelchem_accu_b.par")
#
## simulation of the TMPD radical cation
## EPR spectrum
data.spectrum.sim <-
  eval_sim_EPR_iso(g.iso = 2.00303,
    instrum.params = NULL,
    path_to_dsc_par = tmpd.params.file,
    origin = "winepr",
    nuclear.system = list(
      list("14N", 2, 19.29),
      list("1H", 4, 5.49),
      list("1H", 12, 19.66)
    ),
  lineGL.DeltaB = list(0.48, 0.32),
  lineG.content = 0.5,
)
#
## comparison of both spectra
## by the simulated spectrum offset
## and narrower B-range
present_EPR_Sim_Spec(
  data.spectr.expr = data.spectrum.expr,
  data.spectr.sim = data.spectrum.sim$df,
  Blim = c(3450,3550)
) + plot_theme_NoY_ticks(legend.text =
           ggplot2::element_text(size = 13)
           )

#
## comparison of both spectra
## in overlay mode
present_EPR_Sim_Spec(
  data.spectr.expr = data.spectrum.expr,
  data.spectr.sim = data.spectrum.sim$df,
  Intensity.shift.ratio = NULL,
) + plot_theme_NoY_ticks(legend.text =
           ggplot2::element_text(size = 13)
           )