addClusterings {clusterExperiment} | R Documentation

## Add clusterings to ClusterExperiment object

### Description

Function for adding new clusterings in form of vector (single cluster) or matrix (multiple clusterings) to an existing ClusterExperiment object

### Usage

    ## S4 method for signature 'ClusterExperiment,matrix'
    addClusterings(
      x,
      y,
      clusterTypes = "User",
      clusterLabels = NULL,
      clusterLegend = NULL
    )

    ## S4 method for signature 'ClusterExperiment,ClusterExperiment'
    addClusterings(x, y, transferFrom = c("x", "y"), mergeCEObjects = FALSE)

    ## S4 method for signature 'ClusterExperiment,vector'
    addClusterings(x, y, makePrimary = FALSE, ...)

### Arguments

`x` | a ClusterExperiment object
`y` | additional clusters to add to x. Can be a ClusterExperiment object or a matrix/vector of clusters.
`clusterTypes` | a string describing the nature of the clustering. The values 'clusterSingle', 'clusterMany', 'mergeClusters', 'makeConsensus' are reserved for the clustering coming from the package workflow and should not be used when creating a new object with the constructor.
`clusterLabels` | label(s) for the clusters being added. If `y` a matrix, the column names of that matrix will be used by default, if `clusterLabels` is not given.
`clusterLegend` | a list giving the cluster legend for the clusters added.
`transferFrom` | If x and y are both `ClusterExperiment` objects indicates from which object the clustering info should be taken (regarding merging, dendrogram, etc). Does not affect the order of the clusterings, which will always be the clusterings of x, followed by those of y (along with slots 'clusterType', 'clusterInfo', 'clusterLegend')
`mergeCEObjects` | logical If x and y are both `ClusterExperiment` objects indicates as to whether should try to grab in the information missing from x from y (or vice versa if transferFrom=y).
`makePrimary` | whether to make the added cluster the primary cluster (only relevant if `y` is a vector)
`...` | For `addClusterings`, passed to signature `ClusterExperiment,matrix`. For `[` (subsetting), passed to `SingleCellExperiment` subsetting function.

### Details

addClusterings adds y to x, and is thus not symmetric in the two arguments. In particular, the `primaryCluster`, all of the dendrogram information, the merge information, `coClustering`, and `orderSamples` are all kept from the x object, even if y is a ClusterExperiment.

### Value

A `ClusterExperiment` object.

### Examples

    data(simData)

    cl1 <- clusterSingle(simData, subsample=FALSE,
    sequential=FALSE, mainClusterArgs=list(clusterArgs=list(k=3),
    clusterFunction="pam"))
    cl2 <- clusterSingle(simData, subsample=FALSE,
    sequential=FALSE, mainClusterArgs=list(clusterArgs=list(k=3),
    clusterFunction="pam"))

    addClusterings(cl1, cl2)

[Package clusterExperiment version 2.12.0 Index]