Draw Spectrum — draw_spectrum • metabodecon

Draws a single spectrum. Internally used by plot_spectrum(), which is usually the recommended way to plot spectra. For usage examples see test/testthat/test-draw_spectrum.R.

Usage

draw_spectrum(
  obj,
  foc_rgn = NULL,
  foc_frac = NULL,
  foc_only = TRUE,
  add = FALSE,
  fig_rgn = NULL,
  main = NULL,
  show = TRUE,
  show_d2 = FALSE,
  truepar = NULL,
  mar = c(4.1, 5.1, 0.1, 0.1),
  si_line = list(),
  sm_line = list(),
  sp_line = list(),
  d2_line = list(),
  lc_lines = list(),
  tp_lines = list(),
  cent_pts = list(),
  bord_pts = list(),
  norm_pts = list(),
  bg_rect = list(),
  foc_rect = list(),
  lc_rects = list(),
  tp_rects = list(),
  bt_axis = list(),
  lt_axis = list(),
  tp_axis = list(),
  rt_axis = list(),
  tp_verts = list(),
  lc_verts = list(),
  lgd = list()
)

Arguments

obj

An object of type spectrum or decon2. For details see metabodecon_classes.

foc_rgn

Numeric vector specifying the start and end of focus region in ppm.

foc_frac

Numeric vector specifying the start and end of focus region as fraction of the full spectrum width.

foc_only

Logical. If TRUE, only the focused region is drawn. If FALSE, the full spectrum is drawn.

add

If TRUE, draw into the currently open figure. If FALSE, start a new figure.

fig_rgn

Drawing region in normalized device coordinates as vector of the form c(x1, x2, y1, y2).

main

Main title of the plot. Drawn via title().

show

Logical. If FALSE, the function returns without doing anything.

show_d2

Logical. If TRUE, the second derivative of the spectrum is drawn. Setting this to TRUE changes most of the defaults for the drawing, e.g. by disabling the drawing of anything related to signal intensities and by changing the y-axis label to "Second Derivative".

truepar

Data frame with columns x0, A and lambda containing the true lorentzian that were used to simulate the spectrum. Required if any tp_* argument is set.

mar

Number of lines below/left-of/above/right-of plot region.

si_line, sm_line, lc_lines, sp_line, d2_line, tp_lines

List of parameters passed to lines() when drawing the raw signal intensities, smoothed signal intensities, lorentzian curves found by deconvolution, superposition of lorentzian curves, second derivative and/or true lorentzian curves.

cent_pts, bord_pts, norm_pts

List of parameters passed to points() when drawing the peak center points, peak border points and non-peak points.

bg_rect, lc_rects, foc_rect, tp_rects

List of parameters passed to rect() when drawing the background, lorentzian curve substitutes, focus rectangle and/or true lorentzian curve substitutes.

bt_axis, lt_axis, tp_axis, rt_axis

List of parameters used to overwrite the default values passed to axis() when drawing the bottom, left, top and right axis. In addition to the parameters of axis(), the following additional parameters are supported as well:

text: Description for the axis. Drawn via mtext().
n: Number of tickmarks.
digits: Number of digits for rounding the labels. If a vector of numbers is provided, all numbers are tried, until n unique labels are found. See 'Details'.
sf: Scaling factor. Axis values are divided by this number before the labels are calculated. If you set this to anything unequal 1, you should also choose text in a way that reflects the scaling. E.g. if you set sf = 1e6 you could change the text from "Signal Intensity [au]" to "Signal Intensity [Mau]" or "Signal Intensity [au] / 1e6", with "Mau" meaning "Mega-Arbitrary-Units".

lc_verts, tp_verts

List of parameters passed to abline() when drawing vertical lines at the centers of estimated lorentzian curves and/or true lorentzian curves. Setting tp_verts$show to TRUE requires truepar to be set.

lgd

List of parameters passed to legend() when drawing the legend.

Value

NULL. Called for side effect of plotting.

Details

Parameters bt_axis, lt_axis, tp_axis and rt_axis all support option n and digits, where n = 5 means "Draw 5 tickmarks over the full axis range" and digits = 3 means "round the label shown beside each tickmark to 3 digits". If n is omitted, a suitable value is chosen automatically using axTicks(). If digits is omitted, a default of 2:12 is used. Providing a vector of digits causes each digit to be tried as argument for round(), until a digit is encountered that results in n unique labels. Example:

Assume we have n = 4 and the corresponding calculated tickmark positions are: 1.02421, 1.02542, 1.02663 and 1.02784. If we provide digits = 1:5, the following roundings are tried:

digit	label 1	label 2	label 3	label 4
1	1	1	1	1
2	1.02	1.03	1.03	1.03
3	1.024	1.025	1.027	1.028
4	1.0242	1.0254	1.0266	1.0278
5	1.02421	1.02542	1.02663	1.02784

In the above example the process would stop at digit = 3, because at this point we have n = 4 unique labels (1.024, 1.025, 1.027 and 1.028).

Examples

decon <- deconvolute(sim[[1]], sfr = c(3.55, 3.35))
draw_spectrum(obj = decon)

#> $plt_rgn_ndc
#> [1] 0.1457143 0.9971429 0.1171429 0.9971429
#> 
#> $foc_rgn_ndc
#> [1] 0.9977677 0.1450895 0.1171429 0.9971429
#> 
draw_spectrum(obj = decon, lgd = list(x = "top", bg = NA))

#> $plt_rgn_ndc
#> [1] 0.1457143 0.9971429 0.1171429 0.9971429
#> 
#> $foc_rgn_ndc
#> [1] 0.9977677 0.1450895 0.1171429 0.9971429
#> 
draw_spectrum(obj = decon, foc_rgn = c(3.45, 3.37))
#> $plt_rgn_ndc
#> [1] 0.1457143 0.9971429 0.1171429 0.9971429
#> 
#> $foc_rgn_ndc
#> [1] 0.9982098 0.1446473 0.1171429 0.9971429
#> 
draw_spectrum(obj = decon, fig = c(0.1, 0.4, 0.30, 0.45), add = TRUE)

#> $plt_rgn_ndc
#> [1] 0.2457143 0.3971429 0.4171429 0.4471429
#> 
#> $foc_rgn_ndc
#> [1] 0.3972540 0.2456032 0.4171429 0.4471429
#> 
draw_spectrum(obj = decon, fig = c(0.1, 0.4, 0.05, 0.20), add = FALSE)

#> $plt_rgn_ndc
#> [1] 0.2457143 0.3971429 0.1671429 0.1971429
#> 
#> $foc_rgn_ndc
#> [1] 0.3972540 0.2456032 0.1671429 0.1971429
#> 
draw_spectrum(obj = decon, lc_lines = NULL, lc_rects = NULL, foc_only = FALSE)

#> $plt_rgn_ndc
#> [1] 0.1457143 0.9971429 0.1171429 0.9971429
#> 
#> $foc_rgn_ndc
#> [1] 0.6778571 0.4650000 0.1171429 0.8285104
#>