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Interactive Plot (incl. Zooming, Data Reading...etc) of EPR Spectra

Source: R/plot_EPR_Specs2D_interact.R
plot_EPR_Specs2D_interact.Rd

Interactive visualization of EPR spectra or their integrals based on plotly package. In the first step function takes the essential plot parts as ggplot2, which is subsequently transferred by ggplotly into the final interactive format. Such plots mostly contain buttons in order to zoom, move and select (parts of) the EPR spectra/integrals as well as to display the point values directly within graph/panel. Additionally, plots can be exported into .png image or .html formats (see also plot_EPR_present_interact) and can optionally also contain tools to draw lines, circles or rectangles directly into the plot panel for annotations.

Usage

plot_EPR_Specs2D_interact(
  data.spectra,
  x = "B_mT",
  x.unit = "mT",
  Intensity = "dIepr_over_dB",
  var2nd.series = NULL,
  lineSpecs.form = "derivative",
  line.colors = "darkviolet",
  line.width = 0.75,
  line.type = 1,
  bg.color = "#e5ecf6",
  grid.color = "white",
  border.line.width = 1.2,
  border.line.color = "black",
  legend.title = NULL,
  legend.title.size = NULL,
  axis.title.size = 15,
  axis.text.size = 14
)

Arguments

data.spectra

Spectrum data frame/table object, containing magnetic flux density, \(g\)-value or radio-frequency columns as x variable. They can be labeled as Field, B_mT in mT (or B_G in gauss), see also x parameter/argument. The y/Intensity variable can be labeled as dIepr_over_dB, in case of derivative intensity, or if integrated or simulated spectra intensities are present, they can be labeled accordingly. See also Intensity parameter/argument. For spectral series the second independent variable var2nd.series column (e.g. var2nd.series = "time_s") must be available. In such case, the entire data.spectra must be present in the form of tidy/long table format (see also parameter/argument var2nd.series).

x

Character string, pointing to \(x\)-axis/column quantity in the original data.spectrum like magnetic flux density \(B\), \(Field\), \(g\)-Value or \(RF\) (radio frequency), default: x = "B_mT".

x.unit

Character string pointing to \(x\)-unit of quantity (coming from the original ASCII data, see also column.names parameter) which is to be presented on \(x\)-axis of the EPR spectrum, like "G" ("Gauss"), "mT" ("millitesla"), "MHz" ("megahertz", in the case of ENDOR spectra) or "Unitless" in case of \(g\)-values, default: x.unit = "mT".

Intensity

Character string, corresponding to the intensity column header in the original data.spectrum if other than dIepr_over_dB name/label is used (e.g. for integrated or simulated spectra), default: Intesity = "dIepr_over_dB".

var2nd.series

Character string, referred to name of the second independent variable/quantity column in the original data.spectra (such as time, Temperature, Electrochemical Potential, Microwave Power...etc) altered upon individual experiments. Data must be available in long table (or tidy) format (see also data.spectra argument). Default: var2nd.series = NULL. Otherwise, usually, var2nd.series = "time_s".

lineSpecs.form

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

line.colors

Character string (vector). In case of of SIMPLE SPECTRUM (NOT FOR var2nd.series) ONLY ONE COLOR CHARACTER STRING IS REQUIRED => therefore, default: line.color = "darkviolet". For the SERIES OF SPECTRA CHARACTER COLOR VECTOR WITH THE LENGTH \(\geq 2\) must be DEFINED (e.g. line.colors = c("darkorange","darkblue")).

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".

bg.color

Character string, corresponding to background color of the panel/graph. Available colors are listed on the CSS Color Module Homepage. Default: bg.color = "#e5ecf6" (corresponding to light blue-gray).

grid.color

Character string, corresponding to grid lines color of the panel/graph. Available colors are listed on the CSS Color Module Homepage. Default: grid.color = "white".

border.line.width

Numeric, width (in px) of the graph/plot panel border line, default: border.line.width = 1.2.

border.line.color

Character string, referring to color of the plot graph/panel border line. Available colors are listed on CSS Color Module Homepage. Default: border.line.color = "black".

legend.title

Character string \(\equiv\) title of the legend (if the var2nd.series in NOT NULL). It can be defined either by simple text like legend.title = "Time (s)" or if additional formatting is required, the html markup language, such as legend.title = "<i>Time</i> (s)" or legend.title = "<i>Potential<i> <br> <i>vs</i> Fc/Fc<sup>+</sup> (V)" is used. If a \(\LaTeX\) typesetting is required for the title, please refer to e.g. LaTeX Plotly Tepesetting. Default: legend.title = NULL (in all cases if var2nd.series = NULL).

legend.title.size

Numeric, text size (in px) for the legend title, default: legend.title.size = NULL, which actually corresponds to 13 if not otherwise defined.

axis.title.size

Numeric, text size (in px) for the axis title, default: axis.title.size = 15.

axis.text.size

Numeric, text size (in px) for the axis unit values/descriptions, default: axis.text.size = 14.

Value

Interactive plot object of EPR spectrum/spectra based on plotly package.

See also

Other Visualizations and Graphics: draw_molecule_by_rcdk(), plot_EPR_Specs(), 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(), present_EPR_Sim_Spec()

Examples

## load built-in EPR spectral data
data.file.path <-
  load_data_example(file = "TMPD_specelchem_accu_b.asc")
## spectrum recorded as accumulation of 20 scans
data.epr <-
  readEPR_Exp_Specs(path_to_ASC = data.file.path,
                    col.names = c("B_G", "dIepr_over_dB"),
                    qValue = 3500,
                    norm.vec.add = 20,
                    origin = "winepr")
## interactive plot or screenshot
plot_EPR_Specs2D_interact(data.spectra = data.epr)


#
## loading the built-in CW ENDOR spectrum
## of perinaphthenyl (PNT)
pnt.file.path <- load_data_example("PNT_ENDOR_a.txt")
## read the PNT CW ENDOR data without intensity
## normalization
pnt.endor.data <-
  readEPR_Exp_Specs(pnt.file.path,
                    col.names = c("index",
                                  "RF_MHz",
                                  "dIepr_over_dB"),
                    x.unit = "MHz")
## plotting ENDOR spectrum
plot_EPR_Specs2D_interact(data.spectra = pnt.endor.data,
                          x = "RF_MHz",
                          x.unit = "MHz",
                          line.colors = "darkgreen",
                          bg.color = "cornsilk",
                          grid.color = "darkgrey")


#
if (FALSE) { # \dontrun{
## plot time series EPR spectra = verdazyl radical
## oxidation kinetics (`verdazylRad.kinet.spectr`)
plot_EPR_Specs2D_interact(verdazylRad.kinet.spectr,
  x = "B_G",
  x.unit = "G",
  var2nd.series = "time_s",
  legend.title = "<i>Time</i> (s)",
  line.colors = c("darkorange","darkblue")
  )
} # }