clusteringKmeansNestedHclust {seqsetvis} | R Documentation

## perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments clusters are sorted using hclust on centers the contents of each cluster are sorted using hclust

### Description

perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments clusters are sorted using hclust on centers the contents of each cluster are sorted using hclust

### Usage

    clusteringKmeansNestedHclust(
      mat,
      nclust,
      within_order_strategy = c("hclust", "sort")[2],
      seed = NULL
    )

### Arguments

`mat` | A wide format matrix
`nclust` | the number of clusters
`within_order_strategy` | one of "hclust" or "sort". if hclust, hierarchical clustering will be used. if sort, a simple decreasing sort of rosSums.
`seed` | passed to set.seed() to allow reproducibility

### Value

data.table with 2 columns of cluster info. id column corresponds with input matrix rownames and is sorted within each cluster using hierarchical clusering group column indicates cluster assignment

### Examples

    dt = data.table::copy(CTCF_in_10a_profiles_dt)
    mat = data.table::dcast(dt, id ~ sample + x, value.var = "y" )
    rn = mat$id
    mat = as.matrix(mat[,-1])
    rownames(mat) = rn
    clust_dt = clusteringKmeansNestedHclust(mat, nclust = 3)
    dt = merge(dt, clust_dt)
    dt$id = factor(dt$id, levels = clust_dt$id)
    dt[order(id)]

[Package seqsetvis version 1.8.0 Index]