Intensity pattern of a single or multiple phosphopeptide across the time course and for each condition.

Return the intensity pattern across multiple time points for the provided phosphopeptide IDs.

plotMultiPeptides(
  netPhorceData = netPhorceData,
  foundPepetidesIDs = NULL,
  condition = NULL,
  plotly = TRUE
)

Arguments

netPhorceData

(Required). Processed NetPhorce Object

foundPepetidesIDs

(Required). Single or multiple peptide IDs. Use foundPepetidesIDs with peptideIDList = NULL to extract a full table of available peptide IDs.

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

list of dataframes

Examples

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)
## Provided IDs all matched the IDs in the netPhorce Data
peptideIDs <-
  findPeptideIDs(netPhorceData = netPhorceData,
                 peptideIDList = c("AT1G01320.2_S1349_1",
                                   "AT1G05560.1_S153_1",
                                   "AT1G01320.2_S149_1"))
## Plot Mutliple Phosphopeptide IDs - PLOTLY (Interactive) Version
plotMultiPeptides(netPhorceData = netPhorceData,
                  foundPepetidesIDs = peptideIDs,
                  condition = "Col0",
                  plotly = TRUE)
## Plot Mutliple Phosphopeptide IDs - GGPLOT (Static) Version
plotMultiPeptides(netPhorceData = netPhorceData,
                  foundPepetidesIDs = peptideIDs,
                  condition = "tot3",
                  plotly = FALSE)
}