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Plot a chromatogram as a contour plot

Source: R/plot_chroms.R
plot_chrom_contour.Rd

Plots a single multi-wavelength chromatogram as an image, with retention time on the x axis, wavelength on the y axis, and color encoding absorbance.

Usage

plot_chrom_contour(
  x,
  idx = 1,
  xlim = NULL,
  ylim = NULL,
  scale = c("asinh", "linear"),
  zlim = NULL,
  show_legend = TRUE,
  title = NULL,
  xlab = "",
  ylab = "Wavelength",
  ...
)

Arguments

x

A list of chromatograms in matrix format (timepoints × wavelengths) or a peak_table containing a pointer to a list of chromatograms accessible in the current environment.

idx

Name or numerical index of the chromatogram to plot. Defaults to the first.

xlim

Range of retention times to plot.

ylim

Range of wavelengths to plot.

scale

Color scale: "asinh" (the default) or "linear".

zlim

Range of absorbance values spanned by the color scale. Values outside it are drawn in the end colors. Defaults to the range of the plotted region.

show_legend

Logical. Whether to display a color bar. Defaults to TRUE.

title

Title for plot. Defaults to the name of the chromatogram; "" omits it.

xlab

X label.

ylab

Y label. Defaults to "Wavelength".

...

Additional arguments to graphics::image(), e.g. useRaster = TRUE to speed up rendering of large chromatograms on a regular grid.

Value

No return value.

Details

With scale = "asinh" (the default), color follows asinh(x / s), where s is 1/100 of the largest absolute value in the plotted region, or in zlim when it is given. The scale is linear near zero and logarithmic above s, so peaks up to about 100 times smaller than the tallest one stay visible. The color bar is labeled in absorbance units.

By default each plot is scaled to its own data, so colors cannot be compared between plots. Pass the same zlim to every plot to put them on one scale (see examples).

Side effects

The plot is rendered to the active graphics device.

See also

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

Author

Ethan Bass

Examples

data(Sa_pr)
plot_chrom_contour(Sa_pr, idx = 1)


# one color scale for every sample
zlim <- range(unlist(Sa_pr))
plot_chrom_contour(Sa_pr, idx = 1, zlim = zlim)

plot_chrom_contour(Sa_pr, idx = 2, zlim = zlim)


# the same, zoomed in
zoomed <- crop_chroms(Sa_pr, rt_range = c(12, 13))
plot_chrom_contour(zoomed, idx = 1, zlim = range(unlist(zoomed)))