spectra-plotting: Plotting Spectra
In lgatto/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Description Usage Arguments Value Author(s) Examples

Spectra() can be plotted with one of the following functions

plotSpectra: plots each spectrum in its separate plot by splitting the plot area into as many panels as there are spectra.
plotSpectraOverlay: plots all spectra in x into the same plot (as an overlay).
plotSpectraMirror: plots a pair of spectra as a mirror plot. Parameters x and y both have to be a Spectra of length 1. Matching peaks (considering ppm and tolerance) are highlighted. See common() for details on peak matching. Parameters matchCol, matchLty, matchLwd and matchPch allow to customize how matching peaks are indicated.

plotSpectra(
  x,
  xlab = "m/z",
  ylab = "intensity",
  type = "h",
  xlim = numeric(),
  ylim = numeric(),
  main = character(),
  col = "#00000080",
  labels = character(),
  labelCex = 1,
  labelSrt = 0,
  labelAdj = NULL,
  labelPos = NULL,
  labelOffset = 0.5,
  labelCol = "#00000080",
  asp = 1,
  ...
)

plotSpectraOverlay(
  x,
  xlab = "m/z",
  ylab = "intensity",
  type = "h",
  xlim = numeric(),
  ylim = numeric(),
  main = paste(length(x), "spectra"),
  col = "#00000080",
  labels = character(),
  labelCex = 1,
  labelSrt = 0,
  labelAdj = NULL,
  labelPos = NULL,
  labelOffset = 0.5,
  labelCol = "#00000080",
  axes = TRUE,
  frame.plot = axes,
  ...
)

## S4 method for signature 'Spectra'
plotSpectraMirror(
  x,
  y,
  xlab = "m/z",
  ylab = "intensity",
  type = "h",
  xlim = numeric(),
  ylim = numeric(),
  main = character(),
  col = "#00000080",
  labels = character(),
  labelCex = 1,
  labelSrt = 0,
  labelAdj = NULL,
  labelPos = NULL,
  labelOffset = 0.5,
  labelCol = "#00000080",
  axes = TRUE,
  frame.plot = axes,
  ppm = 20,
  tolerance = 0,
  matchCol = "#80B1D3",
  matchLwd = 1,
  matchLty = 1,
  matchPch = 16,
  ...
)

`x`	a `Spectra()` object. For `plotSpectraMirror` it has to be an object of length 2.
`xlab`	`character(1)` with the label for the x-axis (by default `xlab = "m/z"`).
`ylab`	`character(1)` with the label for the y-axis (by default `ylab = "intensity"`).
`type`	`character(1)` specifying the type of plot. See `plot.default()` for details. Defaults to `type = "h"` which draws each peak as a line.
`xlim`	`numeric(2)` defining the x-axis limits. The range of m/z values are used by default.
`ylim`	`numeric(2)` defining the y-axis limits. The range of intensity values are used by default.
`main`	`character(1)` with the title for the plot. By default the spectrum's MS level and retention time (in seconds) is used.
`col`	color to be used to draw the peaks. Should be either of length 1, or equal to the number of spectra (to plot each spectrum in a different color) or be a `list` with colors for each individual peak in each spectrum.
`labels`	allows to specify a label for each peak. Can be a `character` with length equal to the number of peaks, or, ideally, a `function` that uses one of the `Spectra`'s variables (see examples below). `plotSpectraMirror` supports only `labels` of type function.
`labelCex`	`numeric(1)` giving the amount by which the text should be magnified relative to the default. See parameter `cex` in `par()`.
`labelSrt`	`numeric(1)` defining the rotation of the label. See parameter `srt` in `text()`.
`labelAdj`	see parameter `adj` in `text()`.
`labelPos`	see parameter `pos` in `text()`.
`labelOffset`	see parameter `offset` in `text()`.
`labelCol`	color for the label(s).
`asp`	for `plotSpectra`: the target ratio (columns / rows) when plotting mutliple spectra (e.g. for 20 spectra use `asp = 4/5` for 4 columns and 5 rows or `asp = 5/4` for 5 columns and 4 rows; see `grDevices::n2mfrow()` for details).
`...`	additional parameters to be passed to the `plot.default()` function.
`axes`	`logical(1)` whether (x and y) axes should be drawn.
`frame.plot`	`logical(1)` whether a box should be drawn around the plotting area.
`y`	for `plotSpectraMirror`: `Spectra` object of length 1 against which `x` should be plotted against.
`ppm`	for `plotSpectraMirror`: m/z relative acceptable difference (in ppm) for peaks to be considered matching (see `common()` for more details).
`tolerance`	for `plotSpectraMirror`: absolute acceptable difference of m/z values for peaks to be considered matching (see `common()` for more details).
`matchCol`	for `plotSpectraMirror`: color for matching peaks.
`matchLwd`	for `plotSpectraMirror`: line width (`lwd`) to draw matching peaks. See `par()` for more details.
`matchLty`	for `plotSpectraMirror`: line type (`lty`) to draw matching peaks. See `par()` for more details.
`matchPch`	for `plotSpectraMirror`: point character (`pch`) to label matching peaks. Defaults to `matchPch = 16`, set to `matchPch = NA` to disable. See `par()` for more details.

These functions create a plot.

Johannes Rainer, Sebastian Gibb, Laurent Gatto

ints <- list(c(4.3412, 12, 8, 34, 23.4),
    c(8, 25, 16, 32))
mzs <- list(c(13.453421, 43.433122, 46.6653553, 129.111212, 322.24432),
    c(13.452, 43.5122, 129.112, 322.245))

df <- DataFrame(msLevel = c(1L, 1L), rtime = c(123.12, 124))
df$mz <- mzs
df$intensity <- ints
sp <- Spectra(df)

#### --------------------------------------------- ####
##                   plotSpectra                     ##

## Plot one spectrum.
plotSpectra(sp[1])

## Plot both spectra.
plotSpectra(sp)

## Define a color for each peak in each spectrum.
plotSpectra(sp, col = list(c(1, 2, 3, 4, 5), 1:4))

## Color peaks from each spectrum in different colors.
plotSpectra(sp, col = c("green", "blue"))

## Label each peak with its m/z.
plotSpectra(sp, labels = function(z) format(unlist(mz(z)), digits = 4))

## Rotate the labels.
plotSpectra(sp, labels = function(z) format(unlist(mz(z)), digits = 4),
    labelPos = 2, labelOffset = 0.1, labelSrt = -30)

## Add a custom annotation for each peak.
sp$label <- list(c("", "A", "B", "C", "D"),
    c("Frodo", "Bilbo", "Peregrin", "Samwise"))
## Plot each peak in a different color
plotSpectra(sp, labels = function(z) unlist(z$label),
    col = list(1:5, 1:4))

## Plot a single spectrum specifying the label.
plotSpectra(sp[2], labels = c("A", "B", "C", "D"))


#### --------------------------------------------- ####
##                plotSpectraOverlay                 ##

## Plot both spectra overlaying.
plotSpectraOverlay(sp)

## Use a different color for each spectrum.
plotSpectraOverlay(sp, col = c("#ff000080", "#0000ff80"))

## Label also the peaks with their m/z if their intensity is above 15.
plotSpectraOverlay(sp, col = c("#ff000080", "#0000ff80"),
    labels = function(z) {
        lbls <- format(mz(z)[[1L]], digits = 4)
        lbls[intensity(z)[[1L]] <= 15] <- ""
        lbls
    })
abline(h = 15, lty = 2)

## Use different asp values
plotSpectra(sp, asp = 1/2)
plotSpectra(sp, asp = 2/1)

#### --------------------------------------------- ####
##                plotSpectraMirror                  ##

## Plot two spectra against each other.
plotSpectraMirror(sp[1], sp[2])

## Label the peaks with their m/z
plotSpectraMirror(sp[1], sp[2],
    labels = function(z) format(mz(z)[[1L]], digits = 3),
    labelSrt = -30, labelPos = 2, labelOffset = 0.2)
grid()

## The same plot with a tolerance of 0.1 and using a different color to
## highlight matching peaks
plotSpectraMirror(sp[1], sp[2],
    labels = function(z) format(mz(z)[[1L]], digits = 3),
    labelSrt = -30, labelPos = 2, labelOffset = 0.2, tolerance = 0.1,
    matchCol = "#ff000080", matchLwd = 2)
grid()