GCalignR (version 1.0.7)

plot.GCalign: Plot diagnostics for an GCalign Object

Description

Visualises the aligned data based on four diagnostic plots. One plot shows the distribution of peak numbers per sample in the raw data and after alignment. A second plot gives the distribution of linear shifts that were applied in order to conduct a full alignment of samples with respect to reference. A third sample gives a distribution of the variation in retention times of homologous peaks. The fourth plot shows a frequency distribution of peaks shared among samples.

Usage

# S3 method for GCalign
plot(
  x,
  which_plot = c("all", "shifts", "variation", "peak_numbers", "peaks_shared"),
  ...
)

Value

Depending on the selected plot a data frame containing the data source of the respective plot is returned. If all plots are created, no output will be returned.

Arguments

x

Object of class GCalign, created with align_chromatograms

which_plot

A character defining which plot is created. Options are "shifts", "variation", "peak_numbers" and "peaks_shared". By default all four are created.

...

Optional arguments passed on to methods. See plot, hist and barplot. Note that optional arguments are not passed on when plotting all figures.

Author

Martin Stoffel ([e-mail]) & Meinolf Ottensmann ([e-mail])

Examples

## GCalign object
data("aligned_peak_data")

## All plots are shown by default
plot(aligned_peak_data)

## Distribution of peak numbers
plot(aligned_peak_data, which_plot = "peak_numbers")

## variation of retention times
plot(aligned_peak_data, which_plot = "variation")