mainClustering {clusterExperiment} | R Documentation

## Cluster distance matrix from subsampling

### Description

Given input data, this function will try to find the clusters based on the given ClusterFunction object.

### Usage

    ## S4 method for signature 'character'
    mainClustering(clusterFunction, ...)

    ## S4 method for signature 'ClusterFunction'
    mainClustering(
      clusterFunction,
      inputMatrix,
      inputType,
      clusterArgs = NULL,
      minSize = 1,
      orderBy = c("size", "best"),
      format = c("vector", "list"),
      returnData = FALSE,
      warnings = TRUE,
      ...
    )

    ## S4 method for signature 'ClusterFunction'
    getPostProcessingArgs(clusterFunction)

### Arguments

`clusterFunction` | a `ClusterFunction` object that defines the clustering routine. See `ClusterFunction` for required format of user-defined clustering routines. User can also give a character value to the argument `clusterFunction` to indicate the use of clustering routines provided in package. Type `listBuiltInFunctions` at command prompt to see the built-in clustering routines. If `clusterFunction` is missing, the default is set to "pam".
`...` | arguments passed to the post-processing steps of the clustering. The available post-processing arguments for a `ClusterFunction` object depend on it's algorithm type and can be found by calling `getPostProcessingArgs`. See details below for documentation.
`inputMatrix` | numerical matrix on which to run the clustering or a `SummarizedExperiment`, `SingleCellExperiment`, or `ClusterExperiment` object.
`inputType` | a character vector defining what type of input is given in the `inputMatrix` argument. Must consist of values "diss","X", or "cat" (see details). "X" and "cat" should be indicate matrices with features in the row and samples in the column; "cat" corresponds to the features being numerical integers corresponding to categories, while "X" are continuous valued features. "diss" corresponds to an `inputMatrix` that is a NxN dissimilarity matrix. "cat" is largely used internally for clustering of sets of clusterings.
`clusterArgs` | arguments to be passed directly to the `clusterFUN` slot of the `ClusterFunction` object
`minSize` | the minimum number of samples in a cluster. Clusters found below this size will be discarded and samples in the cluster will be given a cluster assignment of "-1" to indicate that they were not clustered.
`orderBy` | how to order the cluster (either by size or by maximum alpha value). If orderBy="size" the numbering of the clusters are reordered by the size of the cluster, instead of by the internal ordering of the `clusterFUN` defined in the `ClusterFunction` object (an internal ordering is only possible if slot `outputType` of the `ClusterFunction` is `"list"`).
`format` | whether to return a list of indices in a cluster or a vector of clustering assignments. List is mainly for compatibility with sequential part.
`returnData` | logical as to whether to return the `diss` or `x` matrix in the output. If `FALSE` only the clustering vector is returned.
`warnings` | logical as to whether should give warning if arguments given that don't match clustering choices given. Otherwise, inapplicable arguments will be ignored without warning.

### Details

`mainClustering` is not meant to be called by the user. It is only an exported function so as to be able to clearly document the arguments for `mainClustering` which can be passed via the argument `mainClusterArgs` in functions like `clusterSingle` and `clusterMany`.

Post-processing Arguments: For post-processing the clustering, currently only type 'K' algorithms have a defined post-processing. Specifically

- "findBestK"logical, whether should find best K based on average silhouette width (only used if clusterFunction of type "K").

- "kRange"vector of integers to try for k values if findBestK=TRUE. If `k` is given in `clusterArgs`, then default is k-2 to k+20, subject to those values being greater than 2; if not the default is `2:20`. Note that default values depend on the input k, so running for different choices of k and findBestK=TRUE can give different answers unless kRange is set to be the same.

- "removeSil"logical as to whether remove the assignment of a sample to a cluster when the sample's silhouette value is less than `silCutoff`

- "silCutoff"Cutoff on the minimum silhouette width to be included in cluster (only used if removeSil=TRUE).

### Value

If `returnData=FALSE`, mainClustering returns a vector of cluster assignments (if format="vector") or a list of indices for each cluster (if format="list"). Clusters less than minSize are removed. If `returnData=TRUE`, then mainClustering returns a list

- resultsThe clusterings of each sample.

- inputMatrixThe input matrix given to argument `inputMatrix`. Useful if input is result of subsampling, in which case input is the set of clusterings found over subsampling.

### Examples

    data(simData)
    cl1<-mainClustering(inputMatrix=simData, inputType="X",
        clusterFunction="pam",clusterArgs=list(k=3))
    #supply a dissimilarity, use algorithm type "01"
    diss<-as.matrix(dist(t(simData),method="manhattan"))
    cl2<-mainClustering(diss, inputType="diss", clusterFunction="hierarchical01",
        clusterArgs=list(alpha=.1))
    cl3<-mainClustering(inputMatrix=diss, inputType="diss", clusterFunction="pam",
        clusterArgs=list(k=3))

    # run hierarchical method for finding blocks, with method of evaluating
    # coherence of block set to evalClusterMethod="average", and the hierarchical
    # clustering using single linkage:
    # (clustering function requires type 'diss'),
    clustSubHier <- mainClustering(diss, inputType="diss",
        clusterFunction="hierarchical01", minSize=5,
        clusterArgs=list(alpha=0.1,evalClusterMethod="average", method="single"))

    #post-process results of pam -- must pass diss for silhouette calculation
    clustSubPamK <- mainClustering(simData, inputType="X", clusterFunction="pam",
        silCutoff=0, minSize=5, diss=diss, removeSil=TRUE, clusterArgs=list(k=3))
    clustSubPamBestK <- mainClustering(simData, inputType="X", clusterFunction="pam", silCutoff=0,
        minSize=5, diss=diss, removeSil=TRUE, findBestK=TRUE, kRange=2:10)

    # note that passing the wrong arguments for an algorithm results in warnings
    # (which can be turned off with warnings=FALSE)
    clustSubTight_test <- mainClustering(diss, inputType="diss",
       clusterFunction="tight",
       clusterArgs=list(alpha=0.1), minSize=5, removeSil=TRUE)
    clustSubTight_test2 <- mainClustering(diss, inputType="diss",
       clusterFunction="tight",
       clusterArgs=list(alpha=0.1,evalClusterMethod="average"))

[Package clusterExperiment version 2.12.0 Index]