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

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

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')

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