plotNRS {CATALYST} | R Documentation

## Plot non-redundancy scores

### Description

Plots non-redundancy scores (NRS) by feature in decreasing order of average NRS across samples.

### Usage

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

### Arguments

`x` | a `SingleCellExperiment`.
`features` | a character vector specifying which antigens to use for clustering; 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 the color coding; valid values are `namescolData(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)

    plotNRS(sce, features = NULL)   # default: all markers
    plotNRS(sce, features = "type") # type-markers only

[Package CATALYST version 1.14.1 Index]