plot.peak_list

Visually assess integration accuracy by plotting fitted peaks over trace.

Tools for high-throughput analysis of HPLC-DAD/UV
chromatograms (or similar data). Includes functions for preprocessing, alignment,
peak-finding and fitting, peak-table construction, data-visualization, etc.
Preprocessing and peak-table construction follow the rough formula laid out
in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015.
<doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available
using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers
P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic
time warping (VPdtw) (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>).
Peak-finding uses the algorithm by Tom O'Haver
<http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>.
Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape
using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001.
<doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and
suggested workflow.

Ethan Bass

chromatographR

Chromatographic Data Analysis Toolset

plot.peak_list function

<dl><dt>x</dt>
<dd>Peak_list object. Output from the <code>get_peaks</code> function.</dd>
<dt>...</dt>
<dd>Additional arguments to plot function.</dd>
<dt>chrom_list</dt>
<dd>List of chromatograms (retention time x wavelength
matrices)</dd>
<dt>index</dt>
<dd>Index or name of chromatogram to be plotted.</dd>
<dt>lambda</dt>
<dd>Wavelength for plotting.</dd>
<dt>points</dt>
<dd>Logical. If TRUE, plot peak maxima. Defaults to FALSE.</dd>
<dt>ticks</dt>
<dd>Logical. If TRUE, mark beginning and end of each peak. Defaults
to FALSE.</dd>
<dt>a</dt>
<dd>Alpha parameter controlling the transparency of fitted shapes.</dd>
<dt>color</dt>
<dd>The color of the fitted shapes.</dd>
<dt>cex.points</dt>
<dd>Size of points. Defaults to 0.5</dd></dl>

Arguments

Plots a chromatographic trace from the specified chromatogram (<code>chr</code>)
at the specified wavelength (<code>lambda</code>) with fitted peak shapes from the
provided <code>peak_list</code> drawn underneath the curve.

Side effects

Author

Plot fitted peak shapes. — plot.peak_list

<dl>

<dt>x</dt>
<dd>Peak_list object. Output from the <code>get_peaks</code> function.</dd>


<dt>...</dt>
<dd>Additional arguments to plot function.</dd>


<dt>chrom_list</dt>
<dd>List of chromatograms (retention time x wavelength
matrices)</dd>


<dt>index</dt>
<dd>Index or name of chromatogram to be plotted.</dd>


<dt>lambda</dt>
<dd>Wavelength for plotting.</dd>


<dt>points</dt>
<dd>Logical. If TRUE, plot peak maxima. Defaults to FALSE.</dd>


<dt>ticks</dt>
<dd>Logical. If TRUE, mark beginning and end of each peak. Defaults
to FALSE.</dd>


<dt>a</dt>
<dd>Alpha parameter controlling the transparency of fitted shapes.</dd>


<dt>color</dt>
<dd>The color of the fitted shapes.</dd>


<dt>cex.points</dt>
<dd>Size of points. Defaults to 0.5</dd>

</dl>

Plots a chromatographic trace from the specified chromatogram (<code>chr</code>)
at the specified wavelength (<code>lambda</code>) with fitted peak shapes from the
provided <code>peak_list</code> drawn underneath the curve.

plot.peak_list: Plot fitted peak shapes.

Description

Usage

Value

Arguments

Side effects

Author

See Also