inst/shinyApp/app/MethodsFolder/kmeans.R

In IsamBenS/3CClusteringTool: Clustering Tool

fct.parameters <- list("centers"=c(0,10,500,100),"iterations"=c(0,100,1000,100), "nstart"=c(0,1,50,6))
fct.parameters.description <- list("Number of clusters.",
                        "Number of iterations to run to compute the centers of the clusters.",
                        "Number of sets of points to choose. Determines how many times the algorithm should run.")

BRP_BM.kmeans.execute <- function(fcs.file, params = list(50,10,1), markers_col)
{
    k <- min(as.numeric(params[[1]]), nrow(fcs.file@exprs))
    fcs.out.kmeans <- kmeans(fcs.file@exprs[,as.numeric(markers_col)],
							centers=k,
							iter.max=as.numeric(params[[2]]),
							nstart=as.numeric(params[[3]]))
    fcs.labels <- matrix(fcs.out.kmeans$cluster, ncol=1)
    colnames(fcs.labels) <- paste0("cluster_K-Means.",ncol(fcs.file@exprs)+1)

    return(fcs.labels)
}