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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | 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,
...
)
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 |
xlab |
|
ylab |
|
type |
|
xlim |
|
ylim |
|
main |
|
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 |
labels |
allows to specify a label for each peak. Can be a |
labelCex |
|
labelSrt |
|
labelAdj |
see parameter |
labelPos |
see parameter |
labelOffset |
see parameter |
labelCol |
color for the label(s). |
asp |
for |
... |
additional parameters to be passed to the |
axes |
|
frame.plot |
|
y |
for |
ppm |
for |
tolerance |
for |
matchCol |
for |
matchLwd |
for |
matchLty |
for |
matchPch |
for |
These functions create a plot.
Johannes Rainer, Sebastian Gibb, Laurent Gatto
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | 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()
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.