plotNRS: Plot non-redundancy scores

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

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 [e-mail]

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

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.