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Plot Spectrum

Source: R/40_plot.R
plot_spectrum.Rd

Plot a spectrum and zoom in on a specific region. [Experimental]

Usage

plot_spectrum(
  x,
  ...,
  obj = as_v2_obj(x),
  foc_frac = get_foc_frac(obj),
  foc_rgn = get_foc_rgn(obj, foc_frac),
  sub1 = TRUE,
  sub2 = FALSE,
  sub3 = width(foc_rgn) < width(obj$cs),
  mar = NULL,
  frame = FALSE,
  con_lines = TRUE
)

Arguments

x

An object of type spectrum, decon0, decon1 or decon2. For details see metabodecon_classes.

...

Additional arguments passed to draw_spectrum() for every sub figure. See 'Details'.

obj

An object of type spectrum or decon2. Usually auto generated from x, but can be set manually in case the default conversion is not sufficient.

foc_frac

A numeric vector specifying the start and end of the focus region as fraction of the full spectrum width. Only used if foc_rgn is set to NULL.

foc_rgn

A numeric vector specifying the start and end of the focus region in ppm. If set to NULL, foc_frac is used to determine the focus region. If both foc_rgn and are set to NULL, a suitable focus region is chosen automatically. Takes precedence over foc_frac.

sub1, sub2, sub3

List of arguments passed to draw_spectrum() when drawing sub figure 1-3. See 'Details'.

mar

A numeric vector of length 4 passed, which specifies the margins of the plot. Passed to par(). If set to NULL, a suitable value is chosen automatically.

frame

A list of values passed to box() when drawing the frame around plot region. If set to NULL, no frame is drawn.

con_lines

A list of values passed to lines() when drawing the connecting lines between sub figure 1 and the focus rectangle in sub figure 3. See 'Details'. If set to NULL, the connecting lines are not drawn.

Value

NULL. Called for side effect of plotting as sketched in 'Details'.

Details

This function first initializes a new plotting canvas. After that it calls draw_spectrum() multiple times to draw the following sub figures onto the plotting canvas:

  1. The signal intensities in the focus region

  2. The second derivative in the focus region

  3. The signal intensities over all datapoints

The argument lists for the individual calls to draw_spectrum() are determined at runtime and depend on the arguments passed to plot_spectrum() as well as the currently active graphics device. To customize the appearance of the individual sub plots, you can overwrite each value passed to draw_spectrum() by providing a corresponding named element in sub1, sub2 or sub3.

A sketch of the resulting figure is shown below.

 __________________________________________
|        ______________1_____________      |
|       | Sub1: Signal Intensity in  |     |
|       | Focus Region               |     |
|       |             /\             |     |
|       |            /  \            |     |
|       |           /    \  /\       |     |
|     11|          /      \/  \      |7    |
|       |     /\  /            \     |     |
|       |    /  \/              \    |     |
|       |   /                    \   |     |
|       |__/___________0__________\__|     |
|       | Sub2: Second Derivative    |     |
|     11| in Focus Region            |7    |
|       |____________________________|     |
|                      3                   |
|    __________________3_________________  |
|   |  Sub3: Signal Intensity over all   | |
|   |  Datapoints     ________________   | |
| 5 |                | Focus Rectangle|  |1|
|   |     /\         |       /\       |  | |
|   |    /  \        |      /  \/\    |  | |
|   |   /    \   /\  |   /\/      \   |  | |
|   |__/______\_/__\_|__/__________\__|__| |
|______________________5___________________|

Note that the figure created by plot_spectrum() can be part of a multi-figure configuration as created when setting mfrow or mfcol via par(). Example:

_______________________________________
| Plot Spectrum with   | Other Figure  |
| sub3 = TRUE          | Other Figure  |
|      ___________     |  ___________  |
|     | Sub Fig 1 |    | | x      x  | |
|     |___________|    | |      x    | |
|     |_Sub_Fig_2_|    | |      x    | |
|   _________________  | |   x     x | |
|  |    Sub Fig 3    | | |      x    | |
|  |_________________| | |___________| |
|______________________|_______________|
| Some other Figure    | Plot Spectrum |
|                      | sub3 = FALSE  |
|  _________________   |  ___________  |
| |     ___         |  | | Sub Fig 1 | |
| | ___/   \___     |  | |           | |
| |/           \____|  | |___________| |
| |                 |  | | Sub Fig 2 | |
| |_________________|  | |___________| |
|______________________|_______________|

Examples

## 1. Prepare a deconvoluted spectrum as input

spec <- read_spectrum(metabodecon_file("sim/sim_01"))
decon <- generate_lorentz_curves_sim(spec)

## 2.1. Plot the full (non-deconvoluted) spectrum
## 2.2. Remove connecting lines, and focus on a specific region specified in ppm
## 2.3. Show second derivative and focus on a specific region specified as fraction
## 2.4. Change color of focus rectangle and margins of sub figure 1
## 2.5. Hide xlab and show second derivative
## 2.6. Change the figure region for sub figure 1

plot_spectrum(spec, sub1 = FALSE)

plot_spectrum(decon, foc_rgn = c(3.49, 3.45), con_lines = FALSE)

plot_spectrum(decon, sub2 = TRUE, foc_frac = c(0.40, 0.30))

plot_spectrum(decon,
    sub1 = list(mar = c(3, 6, 3, 6), lt_axis = list(col = "violet")),
    foc_rect = list(border = "violet", col = transp("violet")),
    con_lines = list(col = "violet")
)

plot_spectrum(decon,
    sub2 = TRUE,
    sub3 = list(bt_axis = list(text = "")),
    frame = TRUE,
    con_lines = FALSE
)

plot_spectrum(decon, sub1 = list(fig_rgn_npc = c(0,1,.3,1), mar = c(0,5,0,0)))