mergeClusters {CATALYST} | R Documentation

## Manual cluster merging

### Description

`mergeClusters` provides a simple wrapper to store a manual merging inside the input `SingleCellExperiment`.

### Usage

    mergeClusters(x, k, table, id, overwrite = FALSE)

### Arguments

`x` | a `SingleCellExperiment`.
`k` | character string specifying the clustering to merge; valid values are `names(cluster_codes(x))`.
`table` | merging table with 2 columns containing the cluster IDs to merge in the 1st, and the cluster IDs to newly assign in the 2nd column.
`id` | character string used as a label for the merging.
`overwrite` | logical specifying whether to force overwriting should a clustering with name `id` already exist.

### Details

in the following code snippets, `x` is a `SingleCellExperiment` object.

- merging codes are accesible through `cluster_codes(x)$id`

- all functions that ask for specification of a clustering (e.g. `plotAbundances`, `plotMultiHeatmap`) take the merging ID as a valid input argument.

### Value

a `SingleCellExperiment` with newly added cluster codes stored in `cluster_codes(.)$id`.

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### References

Nowicka M, Krieg C, Crowell HL, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

### Examples

    # construct SCE & run clustering
    data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    # merge clusters
    sce <- mergeClusters(sce,
      k = "meta20",
      id = "merging",
      table = merging_table)

    # tabulate manual merging
    table(cluster_ids(sce, k = "merging"))

    # visualize median type-marker expression
    plotExprHeatmap(sce,
      features = "type",
      by = "cluster_id",
      k = "merging",
      bars = TRUE)

[Package CATALYST version 1.18.1 Index]