plotClusterExprs {CATALYST} | R Documentation

## Plot expression distributions by cluster

### Description

Plots smoothed densities of marker intensities by cluster.

### Usage

    plotClusterExprs(x, k = "meta20", features = "type")

### Arguments

`x` | a `SingleCellExperiment`.
`k` | character string specifying which clustering to use; valid values are `names(cluster_codes(x))`.
`features` | a character vector specifying which antigens to include; valid values are `"type"/"state"` for `type/state_markers(x)` if `rowData(x)$marker_class` have been specified; a subset of `rownames(x)`; NULL to use all features.

### Value

a `ggplot` object.

### 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)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    plotClusterExprs(sce, k = "meta8")

[Package CATALYST version 1.16.2 Index]