confounders_lsq_barchart: Confounding factor relative change barchart

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

Confounding factor relative change barchart

Description

A barchart of the relative change (delta) in regression coefficient when potential confounding factors are included, and excluded, from the model. Factors with a large delta are considered to be confounding factors.

Usage

confounders_lsq_barchart(feature_to_plot, threshold = 10, ...)

Arguments

feature_to_plot	(numeric, character, integer) The column name of the feature to be plotted.
threshold	(numeric) A horizontal line is plotted to indicate the threshold. The default is 10.
...	Additional slots and values passed to struct_class.

Value

A confounders_lsq_barchart object. This object has no output slots. See chart_plot in the struct package to plot this chart object.

Inheritance

A confounders_lsq_barchart object inherits the following struct classes:

⁠[confounders_lsq_barchart]⁠ >> ⁠[chart]⁠ >> ⁠[struct_class]⁠

Examples

M = confounders_lsq_barchart(
      feature_to_plot = 1,
      threshold = 10)

D = MTBLS79_DatasetExperiment()
M = filter_by_name(mode='include',dimension='variable',
        names=colnames(D$data)[1:10]) + # first 10 features
    filter_smeta(mode='exclude',levels='QC',
        factor_name='Class') + # reduce to two group comparison
    confounders_clsq(factor_name = 'Class',
        confounding_factors=c('run_order','Batch'))
M = model_apply(M,D)
C = C=confounders_lsq_barchart(feature_to_plot=1,threshold=15)
chart_plot(C,M[3])

computational-metabolomics/structToolbox documentation built on Feb. 21, 2025, 9:53 a.m.