spectra-plotting: Plotting Spectra

In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Plotting Spectra

Description

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 MsCoreUtils::common() for details on peak matching. Parameters matchCol, matchLty, matchLwd and matchPch allow to customize how matching peaks are indicated.

Usage

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,
  ...
)

Arguments

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 MsCoreUtils::common() for more details).
tolerance	for plotSpectraMirror(): absolute acceptable difference of m/z values for peaks to be considered matching (see MsCoreUtils::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.

Value

These functions create a plot.

Author(s)

Johannes Rainer, Sebastian Gibb, Laurent Gatto

Examples

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()

rformassspectrometry/Spectra documentation built on Dec. 19, 2024, 1:05 p.m.