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Plot chromatograms as heatmap

Source: R/plot_chroms.R
plot_chroms_heatmap.Rd

Plots the traces from a list of chromatograms as a heatmap, with one row per chromatogram and color encoding absorbance at a single wavelength. Adapted from VPdtw::plot.VPdtw.

Usage

plot_chroms_heatmap(
  x,
  idx = NULL,
  lambdas = NULL,
  engine = c("base", "ggplot", "plotly"),
  show_legend = TRUE,
  xlim = NULL,
  zlim = NULL,
  legend_position = "topright",
  title = "",
  show_ylabs = FALSE
)

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

A vector of names or numerical indices of the chromatograms to plot. Defaults to all chromatograms.

lambdas

A single wavelength to plot. Required for multi-wavelength chromatograms and optional for one-dimensional ones, where a supplied wavelength must match the column name.

engine

Plotting backend to use. One of "base", "ggplot", or "plotly".

show_legend

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

xlim

Range of retention times to plot.

zlim

Range of intensities spanned by the color scale. Values outside it are drawn in the end colors. Defaults to the range within xlim. Pass the same zlim to several plots to put them on one scale.

legend_position

Position of legend. Defaults to "topright". Cannot be repositioned when using the base plotting engine.

title

Title for plot.

show_ylabs

Logical. Whether to label each row with its chromatogram name. Defaults to FALSE.

Value

A plotly or ggplot object when engine = "plotly" or engine = "ggplot", respectively. No value is returned when engine = "base".

Side effects

If engine == "base", 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_chrom_contour(), plot_chroms(), plot_spectrum(), scan_chrom()

Author

Ethan Bass

Examples

data(Sa_warp)
plot_chroms_heatmap(Sa_warp, lambdas = 210)


# zoomed in, on the color scale of the whole run
zlim <- range(sapply(Sa_warp, function(m) m[, "210"]), na.rm = TRUE)
plot_chroms_heatmap(Sa_warp, lambdas = 210, xlim = c(13, 15), zlim = zlim)