Dotplot displaying the log2 intensity of a single phosphopeptide across the different time points and for each condition.

Return if the input unque ID is in the dataset and filter out current results related to this

plotSinglePeptide(
  netPhorceData = netPhorceData,
  foundPepetidesIDs = NULL,
  plotAll = FALSE,
  plotly = FALSE
)

Arguments

netPhorceData

(Required). Processed NetPhorce Object

foundPepetidesIDs

(Required). Single or Multiple Peptides ID, you can use foundPepetidesIDs with ` peptideIDList = NULL to extract a full table of avaliable peptides.

plotAll

(Optional). If TRUE, all matched peptides provided will be plotted in their individual plots.

plotly

(Required). If TRUE, output an interactive plotly version, else output a static ggplot2 version.

Value

one or multiple ggplot/plotly object(s)

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 the first Phosphopeptide ID - GGPLOT (Static) Version
plotSinglePeptide(netPhorceData = netPhorceData,
                   foundPepetidesIDs = peptideIDs,
                   plotAll = FALSE,
                   plotly = TRUE)
## Plot All Provided Phosphopeptide IDs - PLOTLY (Interactive) Version
plotSinglePeptide(netPhorceData = netPhorceData,
                   foundPepetidesIDs = peptideIDs,
                   plotAll = TRUE,
                   plotly = FALSE)
}