Return the phosphorylation signaling network with the inferred causal relations between the kinases/phosphatases and downstream peptides.
plotNetPhorce(
netPhorceData = netPhorceData,
condition = NULL,
FASTADescription = FALSE
)Processed NetPhorce Object
(Required). Select a specific condition if multiple conditions are present.
(Optional). If TRUE, the hover information of the nodes will return the FASTA header column information for better identification of the phosphopeptides.
A visNetwork object
if (FALSE) {
## 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)
}