plotExprs: Expression densities

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Expression densities

Description

Plots smoothed densities of marker intensities, with a density curve for each sample ID, and curves colored by a cell metadata variable of interest.

Usage

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

Arguments

x	a SingleCellExperiment.
features	character vector specifying which features to invlude; 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 a non-numeric cell metadata column by which to color density curves for each sample; valid values are names(colData(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)
plotExprs(sce)

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