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Plotting Spectra

Source: R/plotting-functions.R
spectra-plotting.Rd

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 = list(),
  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 = list(),
  labelCex = 1,
  labelSrt = 0,
  labelAdj = NULL,
  labelPos = NULL,
  labelOffset = 0.5,
  labelCol = "#00000080",
  axes = TRUE,
  frame.plot = axes,
  ...
)

# S4 method for class 'Spectra'
plotSpectraMirror(
  x,
  y,
  xlab = "m/z",
  ylab = "intensity",
  type = "h",
  xlim = numeric(),
  ylim = numeric(),
  main = character(),
  col = "#00000080",
  labels = list(),
  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. Needs to be a list() with length equal to the number of spectra (each element of the list being a character() with length equal to the number of peaks for that spectrum), 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

Johannes Rainer, Sebastian Gibb, Laurent Gatto, Guillaume Deflandre

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) lapply(mz(z), format, digits = 4))


## Rotate the labels.
plotSpectra(sp, labels = function(z) lapply(mz(z), format, 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 = sp$label,
    col = list(1:5, 1:4))


## Plot a single spectrum specifying the label.
plotSpectra(sp[2], labels = list(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) {
    lapply(seq_along(mz(z)), function(i) {
            lbls <- format(mz(z)[[i]], digits = 4)
            lbls[intensity(z)[[i]] <= 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) list(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) list(format(mz(z)[[1L]], digits = 3)),
    labelSrt = -30, labelPos = 2, labelOffset = 0.2, tolerance = 0.1,
    matchCol = "#ff000080", matchLwd = 2)
grid()