plotClusterExprs {CATALYST}R Documentation

Plot expression distributions by cluster

Description

Plots smoothed densities of arcsinh-transformed marker intensities by cluster.

Usage

plotClusterExprs(x, k = "meta20", features = NULL)

Arguments

x

a SingleCellExperiment.

k

character string. Specifies the clustering to use.

features

character string specifying which features to include. Defaults to NULL (= all features). Alternatively, if the colData(x)$marker_class column is specified, can be one of "type", "state", or "none".

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

# construct SCE & run clustering
data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce)

plotClusterExprs(sce)


[Package CATALYST version 1.10.3 Index]