plotMedExprs {CATALYST} | R Documentation

## Plot median expressions

### Description

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

### Usage

    plotMedExprs(x, ...)

    ## S4 method for signature 'daFrame'
    plotMedExprs(x, k = "meta20", facet = c("antigen",
      "cluster_id"), group_by = "condition", shape_by = NULL)

### Arguments

`x` | a `daFrame`.
`...` | optional arguments.
`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` first.
`group_by` | character string. Has to appear as a column name of `rowData(x)`. Specifies a factor to group samples by.
`shape_by` | character string. Has to appear as a column name of `rowData(x)`. Specifies a factor to shape by.

### Value

a `ggplot` object.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### 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

    data(PBMC_fs, PBMC_panel, PBMC_md)
    re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

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

    # run clustering
    re <- cluster(re)

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

[Package CATALYST version 1.8.7 Index]