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Make mirror plot from peak table

Source: R/plot.peak_table.R
mirror_plot.Rd

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.

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 two 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.

Value

No return value, called for side effects.

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.

Side effects

Plots are rendered to the active graphics device. 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.

See also

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

Author

Ethan Bass

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"))