chromatographR (version 0.4.4)

mirror_plot: Make mirror plot from peak table.

Description

Plots chromatograms as a mirror plot.

Usage

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

Value

No return value, called for side effects.

Arguments

peak_table

The peak table (output from get_peaktable function).

chrom_list

A list of chromatograms in matrix form (timepoints x wavelengths).

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.

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

Ethan Bass

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.

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"))