lcms_plot_chrom_peak_image: Image of Chromatographic Peaks by sample

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

Description

It plots the an image of the chromatographic peaks for each sample. This function is useful if you are interested in knowing the effect of the retention time correction on the chromatographic axis.

Usage

lcms_plot_chrom_peak_image(
  x,
  binSize = 30,
  xlim = NULL,
  log = FALSE,
  xlab = "retention time",
  yaxt = graphics::par("yaxt"),
  main = "Chromatographic peak counts",
  ...
)

Arguments

x	A lcms_dataset.
binSize	Bin size for the the reteincion time axis.
xlim	Retention time axis range. If Null, it uses the complete retention time range.
log	If TRUE, it performs a logarithmic transformation on the data.
xlab	Label for the retention time axis.
yaxt	Options for the y axis. Use the default value.
main	Plot title.
...	Additional parameters for image function.

Value

An image with the detected chromatographic peak, for each sample.

See Also

Other dataset functions: IPO_group_peaks(), find_peaks_cwp(), lcms_dataset_load(), lcms_dataset_save(), lcms_fill_chrom_peaks(), lcms_filter_mz(), lcms_filter_polarity(), lcms_filter_rt_min(), lcms_filter_sample_type(), lcms_meta_add(), lcms_meta_export(), lcms_plot_tics(), lcms_rearrange_datafiles_by_class(), lcms_retention_time_alignment_plot(), lcms_tics(), obiAdjust_Rtime(), peakpicking_optimization(), phData()

Other chromatogram functions: lcms_plot_chrom(), lcms_plot_tics()

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

Examples

## Not run: 
file_name <-  system.file("extdata", "peakdet_align.rds", package = "AlpsLCMS")
dataset <- base::readRDS(file_name)
chr_peak_image <- lcms_plot_chrom_peak_image(dataset, binSize = 5, xlim = NULL, log = FALSE,
                                               xlab = "retention time (min)", yaxt = par("yaxt"))
                                               title(main ="Detected Peaks (Aligned)")

## End(Not run)

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.