mirror_plot: Make mirror plot from peak table.

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

Make mirror plot from peak table.

Description

Plots chromatograms as a mirror plot.

Usage

mirror_plot(
  x,
  chrom_list,
  lambdas = NULL,
  var,
  subset = NULL,
  print_legend = TRUE,
  legend_txt = NULL,
  legend_pos = "topright",
  legend_size = 1,
  mirror = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

Arguments

x	The peak table (output from get_peaktable function).
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 peak_table.
lambdas	The wavelength you wish to plot the traces at.
var	Variable to index chromatograms.
subset	Character vector specifying levels to use (if more than 2 levels are present in var).
print_legend	Logical. Whether to print legend. Defaults to TRUE.
legend_txt	Character vector containing labels for legend.
legend_pos	Legend position.
legend_size	Legend size (cex argument). Default is 1.
mirror	Logical. Whether to plot as mirror or stacked plots. Defaults to TRUE.
xlim	Numerical vector specifying limits for x axis.
ylim	Numerical vector specifying limits for y axis.
...	Additional arguments to matplot function.

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. Can also be used to create simple box-plots to examine the distribution of a peak with respect to variables defined in sample metadata.

Value

No return value, called for side effects.

Side effects

If mirror_plot is TRUE, plots a mirror plot comparing two treatments defined by var and subset (if more than two factors are present in var). Otherwise, if mirror_plot is FALSE, the treatments are plotted in two separate panes.

Author(s)

Ethan Bass

See Also

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

Examples

data(Sa_warp)
data(pk_tab)
path <- system.file("extdata", "Sa_metadata.csv", package = "chromatographR")
meta <- read.csv(path)
pk_tab <- attach_metadata(peak_table = pk_tab, metadata = meta, column="vial")
mirror_plot(pk_tab,lambdas = c("210","260"), var = "trt", mirror = TRUE, 
  col = c("green","blue"))

ethanbass/chromatographR documentation built on April 17, 2025, 10:55 a.m.