Plots the trace and/or spectrum for a given peak in peak.table object, or plots the spectrum a particular retention time for a given chromatogram.
Usage
plot_spectrum(
loc = NULL,
peak_table,
chrom_list,
idx = "max",
lambda = "max",
plot_spectrum = TRUE,
plot_trace = TRUE,
spectrum_labels = TRUE,
scale_spectrum = FALSE,
export_spectrum = FALSE,
verbose = TRUE,
what = c("peak", "rt", "idx", "click"),
engine = c("base", "plotly", "ggplot2"),
chr = NULL,
...
)
Arguments
- loc
The name of the peak or retention time for which you wish to extract spectral data.
- peak_table
The peak table (output from
get_peaktable
).- chrom_list
A list of chromatograms in matrix format (timepoints x wavelengths). If no argument is provided here, the function will try to find the
chrom_list
object used to create the providedpeak_table
.- idx
Numerical index of chromatogram you wish to plot, or "max" to automatically plot the chromatogram with the largest signal.
- lambda
The wavelength you wish to plot the trace at if plot_trace == TRUE and/or the wavelength to be used for the determination of signal abundance.
- plot_spectrum
Logical. If TRUE, plots the spectrum of the chosen peak. Defaults to TRUE.
- plot_trace
Logical. If TRUE, plots the trace of the chosen peak at lambda. Defaults to TRUE.
- spectrum_labels
Logical. If TRUE, plots labels on maxima in spectral plot. Defaults to TRUE.
- scale_spectrum
Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.
- export_spectrum
Logical. If TRUE, exports spectrum to console. Defaults to FALSE.
- verbose
Logical. If TRUE, prints verbose output to console. Defaults to TRUE.
- what
What to look for. Either
peak
to extract spectral information for a certain peak,rt
to scan by retention time,idx
to scan by numeric index, orclick
to manually select retention time by clicking on the chromatogram. Defaults to "peak" mode.- engine
Which plotting engine to use:
base
,ggplot2
, orplotly
.- chr
Deprecated. Please use
idx
instead.- ...
Additional arguments.
Value
If export_spectrum
is TRUE, returns the spectrum as a
data.frame
with wavelengths as rows and a single column encoding the
absorbance (or normalized absorbance, if scale_spectrum
is TRUE)
at each wavelength. If export_spectrum
is FALSE, the output depends on
the plotting engine
. If engine == "plotly"
, returns a plotly
object containing the specified plots. Otherwise, if engine == "base"
,
there is no return value.
Details
Can be used to confirm the identity of a peak or check that a particular column in the peak table represents a single compound. Retention times can also be selected by clicking on the plotted trace if what == 'click'.
Side effects
If
plot_trace
is TRUE, plots the chromatographic trace of the specified chromatogram (chr
), at the specified wavelength (lambda
) with a dotted red line to indicate the retention time given byloc
. The trace is a single column from the chromatographic matrix.If
plot_spectrum
is TRUE, plots the spectrum for the specified chromatogram at the specified retention time. The spectrum is a single row from the chromatographic matrix.