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Plotting of Fitted Spectral Line

Source: R/plot_fit.R
plot_fit.Rd

Plots the data and the fitted lineshape returned by peak_fit() or multipeak_fit(), together with the residuals, and the fitted parameters of each peak.

Usage

plot_fit(
  data,
  title = NULL,
  annotate = TRUE,
  show_fwhm = FALSE,
  ncol = NULL,
  xlab = "Wavelength (nm)",
  ylab = "Intensity (arb. units)",
  caption = TRUE,
  base_size = 11,
  point_size = 1.5,
  point_color = "grey20",
  line_width = 0.8,
  fit_color = "#b2182b",
  pt.size = deprecated(),
  pt.colour = deprecated(),
  pt.shape = deprecated(),
  pt.fill = deprecated(),
  line.size = deprecated(),
  line.colour = deprecated(),
  linetype = deprecated(),
  resid.shape = deprecated(),
  resid.size = deprecated(),
  resid.fill = deprecated(),
  resid.colour = deprecated()
)

Arguments

data

The output of peak_fit() or multipeak_fit().

title

The plot title. A long title is split into a title and a subtitle.

annotate

A logical: write the fitted parameters and the quality of the fit above each panel (TRUE, default).

show_fwhm

A logical: draw the FWHM of each peak as a bar at its half maximum (FALSE, default).

ncol

The number of spectra per row. Default is up to 2.

xlab, ylab

The axis titles. Default are "Wavelength (nm)" and "Intensity (arb. units)". The unit in the parentheses of xlab is that of the center and FWHM in the annotations.

caption

TRUE (default), a caption naming the profiles and the lines drawn; FALSE, no caption; or a caption of your own.

base_size

The size of the text, in points. Default is 11; use the text size of the journal (often 7 to 9 points) for a figure saved at its printed size.

point_size

The size of the data points (default 1.5).

point_color

The color of the data points (default "grey20").

line_width

The width of the fitted curve (default 0.8).

fit_color

The color of the fitted curve (default "#b2182b").

pt.size, pt.colour, pt.shape, pt.fill, line.size, line.colour, linetype, resid.shape, resid.size, resid.fill, resid.colour

[Deprecated] Use point_size, point_color, line_width and fit_color; the other styles are fixed.

Value

A patchwork (ggplot2) object.

Details

The fitted curve is drawn on a fine wavelength grid, so it shows the fitted profile between the measured channels. For multi-peak fits, the individual peak contributions are drawn as dashed lines, numbered at their maximum. The dotted line is the fitted baseline \(y_0\).

Parameters. With annotate = TRUE, the top of each panel gives, for each peak, its center, full width at half maximum (FWHM) and area, with their standard errors, and the quality of the fit: \(R^2\) and the root mean square error (RMSE, the residual standard error). The model is \(y = y_0 + \sum_j A_j f_j(x)\), with \(f_j\) of unit area, so that \(A_j\) is the area of peak \(j\). The FWHM is wG (Gaussian), wL (Lorentzian), or for a Voigt or pseudo-Voigt profile the FWHM of the profile from both (Olivero and Longbothum, 1977, see voigt_fwhm()), its standard error propagated from the covariance of the estimates. With show_fwhm = TRUE, the FWHM of each peak is drawn as a bar at its half maximum. The estimates are rounded to two significant digits of their standard errors; all of them are in the tidied column of the fit.

Residuals. The lower panel gives the residuals, with dashed lines at plus and minus twice the RMSE: a structure in the residuals, beyond these lines or along the wavelength, shows a profile that does not fit the line (such as an asymmetric or self-absorbed line).

When several spectra were fitted, each gets its own fit and residual panels, ncol per row.

References

Olivero, J.J., Longbothum, R.L. (1977). Empirical fits to the Voigt line width: A brief review. Journal of Quantitative Spectroscopy and Radiative Transfer, 17(2):233-236.

See also

peak_fit(), multipeak_fit(), voigt_fwhm()

Author

Christian L. Goueguel

Examples

data(forageLIBS)
mean_spectrum <- colMeans(forageLIBS[-(1:14)])
wl <- as.numeric(names(mean_spectrum))
# the Stark-broadened H-alpha line, with its FWHM
halpha <- tibble::as_tibble(as.list(mean_spectrum[wl > 653.5 & wl < 659.5]))
plot_fit(peak_fit(halpha, profile = "lorentzian"), title = "H-alpha 656.28 nm",
         show_fwhm = TRUE)


# the K I doublet: two Gaussian peaks, for a journal column
doublet <- tibble::as_tibble(as.list(mean_spectrum[wl > 404.1 & wl < 405.0]))
plot_fit(multipeak_fit(doublet, peaks = c(404.414, 404.721), profiles = "gaussian"),
         title = "K I 404.41 and 404.72 nm", base_size = 8)