scatterCompareAssays {pulsedSilac} | R Documentation

## Scatter plot of two conditions for each timepoint of an assay.

### Description

Scatter plot of two conditions/replicates for a selected assay. Timepoints are separated using `facet_wrap`.

### Usage

    scatterCompareAssays(x, ...)

    ## S4 method for signature 'SilacProteinExperiment'
    scatterCompareAssays(
      x,
      conditions,
      assayName,
      returnDataFrame = FALSE,
      conditionCol,
      timeCol
    )

    ## S4 method for signature 'SilacPeptideExperiment'
    scatterCompareAssays(
      x,
      conditions,
      assayName,
      returnDataFrame = FALSE,
      conditionCol,
      timeCol
    )

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

### Arguments

`x` | A `SilacProteinExperiment`, `SilacPeptideExperiment` or a `SilacProteomicsExperiment` object.
`...` | Unused.
`conditions` | A `character` of length 2 indicating which 2 conditions should be compared.
`assayName` | Name of the assay to use in the plot.
`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 `ggplot` object or the `data.frame` that would be used instead in the plot.

### Examples

    data('wormsPE')
    scatterCompareAssays(x = wormsPE,
                         conditions = c('OW40', 'OW450'),
                         assayName = 'ratio',
                         mode = 'protein')

[Package pulsedSilac version 1.1.4 Index]