plotDistributionAssay {pulsedSilac} | R Documentation

## Distribution of assay data per condition and timepoint.

### 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')

[Package pulsedSilac version 1.9.1 Index]