FlowSOM (version 1.0.0)

Purity: Purity of a clustering result

Description

Compute mean weighted purity of a clustering result in comparison with true cluster labels

Usage

Purity(realClusters, predictedClusters, weighted=TRUE)

Arguments

realClusters

array with real cluster values

predictedClusters

array with predicted cluster values

weighted

logical. Should the mean be weighted depending on the number of points in the predicted clusters

Value

See Also

FMeasure

Examples

    # Read from file, build self-organizing map and minimal spanning tree
    fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
    flowSOM.res <- ReadInput(fileName, compensate=TRUE,transform=TRUE,
                            scale=TRUE)
    flowSOM.res <- BuildSOM(flowSOM.res,colsToUse=c(9,12,14:18))
    flowSOM.res <- BuildMST(flowSOM.res)
    
    # Apply metaclustering
    metacl <- MetaClustering(flowSOM.res$map$codes,"metaClustering_consensus",
                            max=10)
    
    # Get the manually gated labels using a gatingML file 
    # and the flowUtils library
    ff <- read.FCS(fileName)
    ff_c <- compensate(ff,ff@description$SPILL)
    colnames(ff_c)[8:18] <- paste("Comp-",colnames(ff_c)[8:18],sep="")
    library(flowUtils)
    flowEnv <- new.env()
    gatingFile <- system.file("extdata","manualGating.xml", 
                            package="FlowSOM")
    read.gatingML(gatingFile, flowEnv) 
    filterList <- list( "B cells" = flowEnv$ID52300206,
                    "ab T cells" = flowEnv$ID785879196,
                    "yd T cells" = flowEnv$ID188379411,
                    "NK cells" = flowEnv$ID1229333490,
                    "NKT cells" = flowEnv$ID275096433
                    )
    results <- list()
    for(cellType in names(filterList)){
        results[[cellType]] <- filter(ff_c,filterList[[cellType]])@subSet
    }
    manual <- rep("Unknown",nrow(ff))
    for(celltype in names(results)){
        manual[results[[celltype]]] <- celltype
    }
    
    # Test the purity of the nodes
    Purity(manual,metacl[flowSOM.res$map$mapping[,1]])