scatterCompareAssays: Scatter plot of two conditions for each timepoint of an...

Description Usage Arguments Value Examples

Description

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

Usage

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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

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

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