plotHistBox: Plot the Distribution of the Intensity Data

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Plot the Distribution of the Intensity Data

Description

The histogram and/or boxplot of the intensity data for each time point after normalization. The function generates a ggplot plot.

Usage

plotHistBox(
  netPhorceData = netPhorceData,
  condition = NULL,
  histogram = TRUE,
  boxplot = TRUE
)

Arguments

netPhorceData	(Required). Processed NetPhorce Object
condition	(Required). Select a specific condition from your experiment.
histogram	(Optional). Enable the histogram Plot. If the boxplot parameter is also TRUE, a side-by-side plot will be generated.
boxplot	(Optional). Enable the boxplot. If the histogram parameter is also TRUE, a side-by-side plot will be generated.

Value

A ggplot 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)
## Side-by-side Plot
plotHistBox(netPhorceData = netPhorceData,
             condition = "tot3",
             histogram = TRUE,
             boxplot = TRUE)
## Boxplot Only
plotHistBox(netPhorceData = netPhorceData,
             condition = "Col0",
             histogram = FALSE,
             boxplot = TRUE)
## Histogram Only
plotHistBox(netPhorceData = netPhorceData,
             condition = "tot3",
             histogram = TRUE,
             boxplot = FALSE)

## End(Not run)

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