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Plot Adjustment Results

Source: R/normalization_correction.R
plotAdjustmentResults.Rd

plotAdjustmentResults generates plots to visualize the results of phosphoproteome adjustment.

Usage

plotAdjustmentResults(maeData, normalization = FALSE)

Arguments

maeData

A MultiAssayExperiment object containing phosphoproteome and full proteome data.

normalization

A logical value indicating whether normalization was performed. Default is FALSE.

Value

A list containing:

ratioTrendPlot

A ggplot2 object showing the line plot of PP/FP ratios for features present in all samples.

ratioBoxplot

A ggplot2 object showing the box plot of PP/FP ratios before and after adjustment.

ppBoxplot

A ggplot2 object showing the box plot of phosphorylation intensities in PP samples before and after adjustment.

Details

The function performs the following steps:

  1. Checks if the adjustment factor is present in the sample annotation.

  2. Calculates the ratio matrix before and after adjustment.

  3. Creates a trend line plot for features present in all samples.

  4. Creates box plots of the PP/FP ratios and phosphorylation intensities before and after adjustment.