plotExprs: Expression densities

Description Usage Arguments Value Author(s) References Examples

View source: R/plotExprs.R

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

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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 helena.crowell@uzh.ch

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

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CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.