Plot Heatmap Based on the Clusters Verified from the findClusters function

generate Heatmap Based on the clusters matched to the netPhorce Data from findUniqueIDs() function

plotClustersHeatmap(
  netPhorceData = netPhorceData,
  foundClusterIDs = NULL,
  plotly = TRUE
)

Arguments

netPhorceData

(Required). Processed netPhorce Object

foundClusterIDs

(Required). Output from the findClusters function. If nothing in the “MatchedClusters” vector, no plot will be generated.

plotly

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

Value

a ggplot/plotly object

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)
## Returns all available peptides along with IDs from Significant Set
clusterIDs_Sig <-
  findClusters(netPhorceData = netPhorceData,
               clusterIDs = c(0),
               heatmapType = "Significant",
               minQVal = 0.1,
               verbose = TRUE)
## Returns all available peptides Identify Cluster IDs from “AbsencePresence” Set
clusterIDs_AbsPrs <-
  findClusters(netPhorceData = netPhorceData,
               clusterIDs = c(1, 2),
               heatmapType = "AbsencePresence",
               verbose = TRUE)
## Plotting Significant Heatmap - PLOTLY Version
plotClustersHeatmap(netPhorceData = netPhorceData,
                    foundClusterIDs = clusterIDs_Sig,
                    plotly = TRUE)
## Plotting Significant Heatmap - GGPLOT version
plotClustersHeatmap(netPhorceData = netPhorceData,
                    foundClusterIDs = clusterIDs_AbsPrs,
                    plotly = FALSE)
}