plotDistributionAssay: Distribution of assay data per condition and timepoint.

Description Usage Arguments Value Examples

Description

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

Usage

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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

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

marcpaga/pulsedSilac documentation built on March 11, 2020, 8:49 p.m.