clusteringOPtions: Performs analysis of different cutoff vaules for a BH-SNE...

In sdrowland/RSMod: Creates a 2D or 3D mapping of RNA-Seq Data

Usage

clusteringOPtions(cluster, dim)

Arguments

cluster
dim

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (cluster, dim) 
{
    if (dim == 2) {
        rdis.test = as.matrix(cluster[, c("x", "y")])
        set.seed(0)
        chec = data.frame(matrix(ncol = 0, nrow = 0))
        for (i in seq(5, 100, 5)) {
            test.hd = hdbscan(rdis.test, minPts = i)
            che = as.data.frame(cbind(max(test.hd$cluster), i))
            chec = rbind(chec, che)
        }
        colnames(chec) = c("Modules", "Cutoff Value")
    }
    if (dim == 3) {
        rdis.test = as.matrix(cluster[, c("x", "y", "z")])
        set.seed(0)
        chec = data.frame(matrix(ncol = 0, nrow = 0))
        for (i in seq(5, 100, 5)) {
            test.hd = hdbscan(rdis.test, minPts = i)
            che = as.data.frame(cbind(max(test.hd$cluster), i))
            chec = rbind(chec, che)
        }
        colnames(chec) = c("Modules", "Cutoff Value")
    }
    return(chec)
  }

sdrowland/RSMod documentation built on July 17, 2021, 7:16 p.m.