plotNetPhorce: A VisNetwork plot of the inferred network

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

A VisNetwork plot of the inferred network

Description

Return the phosphorylation signaling network with the inferred causal relations between the kinases/phosphatases and downstream peptides.

Usage

plotNetPhorce(
  netPhorceData = netPhorceData,
  condition = NULL,
  FASTADescription = FALSE
)

Arguments

netPhorceData	Processed NetPhorce Object
condition	(Required). Select a specific condition if multiple conditions are present.
FASTADescription	(Optional). If TRUE, the hover information of the nodes will return the FASTA header column information for better identification of the phosphopeptides.

Value

A visNetwork 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)
## Confirm the correct Kinase/Phosphotase information for the data
netPhorceData <- validateKinaseTable(netPhorceData = netPhorceData,
                                     defaultKinaseTable = TRUE,
                                     abbrev = "Ath")
## Evaluate the netPhorce object with regulation thresholds
netPhorceData <- regulationCheck(netPhorceData = netPhorceData,
                                 upReg = 0.25,
                                 downReg = 0.25,
                                 absMinThreshold = 0.1,
                                 qValueCutOff = 0.05,
                                 verbose = TRUE)
## Network Analysis
netPhorceData <- networkAnalysis(netPhorceData = netPhorceData,
                               requestPlotData = TRUE)
## VisNetwork Plot with FASTA header information included
plotNetPhorce(netPhorceData = netPhorceData,
              condition = "tot3",
              FASTADescription = TRUE)

## End(Not run)

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