plotMedExprs {CATALYST} | R Documentation

## Plot median expressions

### Description

Plots median marker expressions across samples computed on arcsinh-transformed intensities.

### Usage

    plotMedExprs(
      x,
      k = "meta20",
      facet = c("antigen", "cluster_id"),
      group_by = "condition",
      shape_by = NULL
    )

### Arguments

`x` | a `SingleCellExperiment{SingleCellExperiment}`.
`k` | character string. Specifies the clustering to use. If `facet = "antigen"`, this argument will be ignored.
`facet` | `"antigen"` or `"cluster_id"`. Note that the latter requires having run `cluster`.
`group_by` | character string specifying a `colData(x)` column to group samples by.
`shape_by` | character string specifying a `colData(x)` column to shape samples by.

### Value

a `ggplot` object.

### Author(s)

Helena Lucia Crowell

### References

Nowicka M, Krieg C, 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
    data(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)

    # plot median expressions
    plotMedExprs(sce, shape_by = "patient_id")

    # run clustering
    sce <- cluster(sce)

    # plot median expressions across clusters
    plotMedExprs(sce, facet = "cluster_id", k = "meta8")

[Package CATALYST version 1.10.3 Index]