lcms_plot_chrom: Base peak chromatogram

In sipss/NIHSlcms: Signal processing of LC-MS metabolomics

Description

Base peak chromatograms with retention time axis in minutes.

Usage

lcms_plot_chrom(chromatogram_object, treatment_col, rtlim = NULL)

Arguments

chromatogram_object	A XChromatograms object.
treatment_col	Color code by groups.
rtlim	Retention time boundaries (e.g. c(4,8)).

Value

A base peak chromatogram.

See Also

Other chromatogram functions: lcms_plot_chrom_peak_image(), lcms_plot_tics()

Other visualization functions: lcms_peak_table_boxplots(), lcms_peak_table_pca(), lcms_plot_chrom_peak_image(), lcms_plot_tics(), lcms_retcorgroup_optimization(), lcms_retention_time_alignment_plot(), peakpicking_optimization()

Examples

## Not run: 
file_name <- system.file("extdata",
                         "dataset_pos.rds",
                          package = "AlpsLCMS")
dataset <- lcms_dataset_load(file_name)
treatment_col <- scales::hue_pal()(length(unique(dataset$treatment)))
names(treatment_col) <- unique(dataset$treatment)
base_peaks <- xcms::chromatogram(dataset, aggregationFun = "max")
lcms_plot_chrom(base_peaks, treatment_col, rtlim = c(4, 8))

## End(Not run)

sipss/NIHSlcms documentation built on May 13, 2021, 6:19 p.m.