plotClusterExprs: Plot expression distributions by cluster

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Plot expression distributions by cluster

Description

Plots smoothed densities of marker intensities by cluster.

Usage

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

Arguments

x	a SingleCellExperiment.
k	character string specifying which clustering to use; valid values are names(cluster_codes(x)).
features	a character vector specifying which antigens to include; 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.

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

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

plotClusterExprs(sce, k = "meta8")

HelenaLC/CATALYST documentation built on April 1, 2024, 3:16 a.m.