plotExprs {CATALYST} | R Documentation

## Expression densities

### Description

Plots smoothed densities of marker intensities, with a density curve for each sample ID, and curves colored by a cell metadata variable of interest.

### Usage

    plotExprs(x, features = NULL, color_by = "condition", assay = "exprs")

### Arguments

`x` | a `SingleCellExperiment`.
`features` | character vector specifying which features to invlude; 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.
`color_by` | character string specifying a non-numeric cell metadata column by which to color density curves for each sample; valid values are `names(colData(x))`.
`assay` | character string specifying which assay data to use; valid values are `assayNames(x)`.

### 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

    data(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    plotExprs(sce)

[Package CATALYST version 1.14.1 Index]