renameClusters {clusterExperiment} | R Documentation

## Change assigned names or colors of clusters

### Description

Change the assigned names or colors of the clusters in a clustering stored in the clusterLegend slot of the object.

### Usage

    ## S4 method for signature 'ClusterExperiment,character'
    renameClusters(
      object,
      value,
      whichCluster = "primary",
      matchTo = c("name", "clusterIds")
    )

    ## S4 method for signature 'ClusterExperiment,character'
    recolorClusters(
      object,
      value,
      whichCluster = "primary",
      matchTo = c("name", "clusterIds")
    )

### Arguments

`object` | a ClusterExperiment object.
`value` | The value to be substituted in the corresponding slot. See the slot descriptions in `ClusterExperiment` for details on what objects may be passed to these functions.
`whichCluster` | argument that can be a single numeric or character value indicating the single clustering to be used. Giving values that result in more than one clustering will result in an error. See details of `getClusterIndex`.
`matchTo` | whether to match to the cluster name (`"name"`) or internal cluster id (`"clusterIds"`)

### Value

`renameClusters` changes the names assigned to clusters within a clustering

`recolorClusters` changes the colors assigned to clusters within a clustering

### Examples

    #create CE object
    data(simData)
    cl1 <- clusterSingle(simData, subsample=FALSE,
    sequential=FALSE, mainClusterArgs=list(clusterArgs=list(k=3),
    clusterFunction="pam"))
    #Give names to the clusters
    clusterLegend(cl1)
    cl1<-renameClusters(cl1, c("1"="A","2"="B","3"="C"), matchTo="clusterIds")
    clusterLegend(cl1)
    # Change name of single one
    cl1<-renameClusters(cl1, c("1"="D"), matchTo="clusterIds")
    clusterLegend(cl1)
    # Match to existing name, rather than clusterId
    cl1<-renameClusters(cl1, c("B"="N"), matchTo="name")
    clusterLegend(cl1)
    # Change colors in similar way
    cl1<-recolorClusters(cl1, c("N"="red"),matchTo=c("name"))
    clusterLegend(cl1)

[Package clusterExperiment version 2.12.0 Index]