lcms_peak_table_boxplots: Boxplots for the significant peak table features

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

Description

It performs boxplots for any of significant features found in a peak table. All the boxplots are stored in a directory /Boxplots/Boxplot_spectra_.

Usage

lcms_peak_table_boxplots(MAIT.object = NULL, treatment_col)

Arguments

MAIT.object	MAIT object where it is found an annotated peak table.
treatment_col	Treatment for the samples.

Value

BoxPlots are stored in folders associated to their corresponding spectra. No explicit plot is produced by the device.

See Also

Other metabolite identification functions: lcms_identify_metabolites(), lcms_peak_annotation(), lcms_peak_table_pca(), lcms_raw_data(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_to_mait(), lcms_write_parameter_table()

Other dataset_peak_table functions: lcms_dataset_load(), lcms_identify_metabolites(), lcms_peak_annotation(), lcms_peak_table_pca(), lcms_plot_tics(), lcms_raw_data(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_tics(), lcms_to_mait()

Other statistical functions: lcms_peak_table_pca()

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

Examples

## Not run: 
file_name_1 <-  system.file("extdata","peak_table_sig_ann.rds", package = "AlpsLCMS")
peak_table <- base::readRDS(file_name_1)
file_name_2 <-  system.file("extdata","dataset_pos_rt_rs.rds", package = "AlpsLCMS")
dataset <-  base::readRDS(file_name_2)
treatment_col <- scales::hue_pal()(length(unique(dataset$treatment)))
lcms_peak_table_boxplots(peak_table,
                         treatment_col = treatment_col)

## End(Not run)

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