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Plotting Integrated Forms of EPR Spectra Acquired by eval_integ_EPR_Spec

Source: R/plot_EPR_Specs_integ.R
plot_EPR_Specs_integ.Rd

Visualization (static plots based on ggplot2) of integrated EPR spectra coming as data frame outputs from eval_integ_EPR_Spec.

Usage

plot_EPR_Specs_integ(
  data.spectra.integ,
  B = "B_G",
  B.unit = "G",
  Blim = NULL,
  ylim = NULL,
  slct.integs = c("single_Integ", "baseline_Integ_fit", "single_Integ_correct"),
  line.width = 0.75,
  line.type = 1,
  axis.title.size = 15,
  axis.text.size = 14,
  legend.title.size = 13,
  legend.text.size = 11,
  separate.integs = FALSE,
  separate.integ.scales = NULL,
  output.df = FALSE
)

Arguments

data.spectra.integ

Data frame object, inherited output from the eval_integ_EPR_Spec, if output.vecs = FALSE (argument from the latter), corresponding to data frame including the original EPR spectral data and the integral(s).

B

Character string, pointing to magnetic flux density column of the original (data.spectra.integ) data frame, either in "millitesla" or in "gauss", that is B = "B_G" (default) or B = "B_mT" or B = "Bsim_G" to include simulated EPR spectra as well.

B.unit

Character string, denoting the magnetic flux density unit e.g. B.unit = "G" (gauss, default), B.unit = "mT" (millitesla) or B.unit = T (tesla).

Blim

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

ylim

Numeric vector, corresponding to lower and upper limit of the \(y\)-axis scale (e.g. ylim = c(-1e-4,1e-3)). This doesn't apply for separated integrals (if separate.integs = TRUE) and works only in overlay mode (in one graph/panel). Default: ylim = NULL corresponding to the entire \(y\)-range of presented integrals.

slct.integs

Character string vector, pointing to selected integrals/columns/variables (of the original data.spectra.integ data frame) to be presented in the actual plot. Default: slct.integs = c("single_Integ","baseline_Integ_fit","single_Integ_correct").

line.width

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

line.type

Character string or integer, corresponding to width of the (spectral) line(s). Following types can be specified: 0 = "blank", 1 = "solid" (default), 2 = "dashed", 3 = "dotted", 4 = "dotdash", 5 = "longdash" and 6 = "twodash".

axis.title.size

Numeric, axis text title size in pt. Default: axis.title.size = 15.

axis.text.size

Numeric, text size in pt for the axes unit values/descriptions, default: axis.text.size = 14.

legend.title.size

Numeric, legend text title size in pt,default: legend.title.size = NULL, actually corresponding to 13/13pt.

legend.text.size

Numeric, legend text size in pt, default: legend.text.size = NULL, actually corresponding to 11/11pt.

separate.integs

Logical, should be the integrals presented in overlay mode (in one graph/panel) or on separated panels (by facet_wrap, see also the next argument) ? Default: separate.integs = FALSE (integrals are presented in overlay mode).

separate.integ.scales

Character string related to \(y\)-axes scales, unless the separate.integs = FALSE, inherited from facet_wrap. Following expressions are available => "fixed", "free" or in one dimension "free_x" or "free_y". Default: separate.integ.scales = NULL in case of separate.integs = FALSE.

output.df

Logical, whether a transformed data.spectra.integ data frame into tidy/long table format is required for additional processing or plotting. Default: output.df = TRUE.

Value

Depending on output.df argument, function returns plot object including all selected integrated EPR spectra (output.df = FALSE,default) or list (output.df = TRUE) consisting of

df

Data frame object with intensities of all selected integrals and magnetic flux density \(B\) variables/columns in tidy/long table format.

plot

Plot object showing all integrated EPR spectra corresponding to df.

See also

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

Examples

## loading the package built-in example
TMPD.data.path <-
  load_data_example(file = "TMPD_specelchem_accu_b.asc")
TMPD.data <-
  readEPR_Exp_Specs(TMPD.data.path,
                    col.names = c("B_G","dIepr_over_dB"),
                    qValue = 3500,
                    norm.vec.add = c(20,0.001),
                    origin = "winepr")
## integration of the `TMPD` EPR spectrum
TMPD.data.integs <-
  eval_integ_EPR_Spec(TMPD.data,sigmoid.integ = TRUE)
#
## plotting integrals in overlay mode
plot_EPR_Specs_integ(TMPD.data.integs,
  slct.integs = c("single_Integ",
                  "sigmoid_Integ"),
  B = "B_mT",
  B.unit = "mT"
  )

#
## separate integrals within the plot
plot_EPR_Specs_integ(TMPD.data.integs,
  slct.integs = c("single_Integ",
                  "sigmoid_Integ"),
  B = "B_mT",
  B.unit = "mT",
  separate.integs = TRUE,
  separate.integ.scales = "free_y"
  )