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Plot matched peak pairs

Source: R/plot.peak_list.R
plot.matched_peak_list.Rd

Shows how peaks in each sample were matched to the reference by match_peaks.

Usage

# S3 method for class 'matched_peak_list'
plot(x, idx = NULL, type = c("ladder", "scatter"), ...)

# S3 method for class 'matched_peak_list_set'
plot(x, ...)

Arguments

x

A matched_peak_list object from match_peaks, or a matched_peak_list_set, whose wavelengths are plotted in turn.

idx

Integer or character vector of sample indices or names to plot. Defaults to all non-reference samples.

type

Plot type, either "ladder" (default) or "scatter". See Details.

...

Additional arguments passed to plot for type = "ladder", such as xlim to zoom in on part of the run.

Value

Invisibly returns x.

Details

With type = "ladder" (the default), each sample gets one row, with retention time on the x-axis. Dotted vertical lines mark the reference peaks, and a short tick marks each one in every row. A matched sample peak is drawn as a point filled by its spectral correlation with the reference peak, joined to the reference tick by a horizontal bar, so the length and direction of the bar show the retention time shift. A tick without a bar is a reference peak left unmatched in that sample, and an open circle is a sample peak left unmatched. Where a bar would overlap another bar or run through an unmatched peak, it is lifted slightly above its row.

With type = "scatter", each sample gets its own panel, plotting every candidate pair (a pair within the retention time window and above the spectral cutoff) at its reference and sample retention times, so retention time drift shows as distance from the \(y = x\) diagonal. Candidate pairs are colored by spectral correlation, matched pairs are outlined in black, and unmatched peaks are marked on the axes.

See also

match_peaks, get_peaktable

Other visualization functions: boxplot.peak_table(), mirror_plot(), plot.chrom_list(), plot.peak_list(), plot.peak_table(), plot_all_spectra(), plot_chrom_contour(), plot_chroms(), plot_chroms_heatmap(), plot_spectrum(), scan_chrom()

Author

Ethan Bass