plotNRS {CATALYST}R Documentation

Plot non-redundancy scores

Description

Plots non-redundancy scores (NRS) by features in decreasing order.

Usage

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

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)).

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)
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 1.10.3 Index]