plotDistribution: Plot the Distribution of the Intensity Data

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Plot the Distribution of the Intensity Data

Description

Boxplots of the intensity data for each time point, condition, and replicate before and after variance stabilizing normalization (vsn). The function generates a ggplot object by default. An interactive plotly version (used on our Shiny application) is included if plotly = TRUE is set.

Usage

plotDistribution(
  netPhorceData = netPhorceData,
  condition = NULL,
  plotly = FALSE
)

Arguments

netPhorceData	(Required). Processed netPhorce Object
condition	(Required). Select a specific condition from your experiment.
plotly	(Required). If TRUE, output an interactive plotly version, else output a static ggplot2 version.

Value

a ggplot/plotly object

Examples

## Not run: 
## Loading Two Conditions Example
data("twoConditionsExample")
## Identify the Key Columns
identifiedCols <- confirmColumnNames(rawMaxQuant = twoConditionsExample,
                                    positionCol = "Position",
                                    reverseCol = "Reverse",
                                    localizationProbCol = "Localization prob",
                                    potentialContaminationCol = "Potential contaminant",
                                    aminoAcidCol = "Amino acid",
                                    uniqueIDCol = "Protein",
                                    seqWindowIDCol = "Sequence window",
                                    fastaIDCol = "Fasta headers")
## Identify the Intensity Columns with Condition, Time Point and Replication Information
intensityCols <- confirmIntensityColumns(rawMaxQuant = twoConditionsExample,
                                         intensityPattern = "con_time_rep",
                                         verbose = TRUE)
## Process the data based on the identified columns
netPhorceData <- processData(rawMaxQuant = twoConditionsExample,
                             processedColNames = identifiedCols,
                             processedIntensity = intensityCols,
                             minReplication = 3,
                             minLocalProb = 0.75)
## Generate Distribution Plot – GGPLOT version (Static)
plotDistribution(netPhorceData = netPhorceData,
                 condition = NULL,
                 plotly = FALSE)
## Generate Distribution Plot – PLOTLY version (Interactive)
plotDistribution(netPhorceData = netPhorceData,
                 condition = NULL,
                 plotly = TRUE)

## End(Not run)

ksong4/NetPhorce documentation built on March 24, 2023, 12:51 p.m.