plotDistributionAssay: Distribution of assay data per condition and timepoint.

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

Plot the distribution of the data stored in an assay using boxplots or density distributions.

Usage

plotDistributionAssay(x, ...)

## S4 method for signature 'SilacProteinExperiment'
plotDistributionAssay(
  x,
  assayName,
  plotType = "boxplot",
  returnDataFrame = FALSE,
  conditionCol,
  timeCol
)

## S4 method for signature 'SilacPeptideExperiment'
plotDistributionAssay(
  x,
  assayName,
  plotType = "boxplot",
  returnDataFrame = FALSE,
  conditionCol,
  timeCol
)

## S4 method for signature 'SilacProteomicsExperiment'
plotDistributionAssay(
  x,
  assayName,
  mode = "protein",
  plotType = "boxplot",
  returnDataFrame = FALSE,
  conditionCol,
  timeCol
)

Arguments

x	A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.
...	Unused.
assayName	Name of the assay to use in the plot.
plotType	A character indicating which geometry to plot: 'boxplot' or 'density'. (default = 'density')
returnDataFrame	A logical indicating if the data.frame used for the plot should be returned instead.
conditionCol	A character, which indicates the column name in colData(x) that defines the different experiment conditions.
timeCol	A character, which indicates the column name in colData(x) that defines the different timepoints.
mode	A character indicating which level of data to use, either "protein" or "peptide". Only relevant for ProteomicsExperiment inputs.

Value

A ggplot2 object or a data.frame with the data that would be plotted.

Examples

data('wormsPE')
plotDistributionAssay(wormsPE, assayName = 'ratio')

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.