plotDR {CATALYST}R Documentation

Plot reduced dimensions

Description

Dimension reduction plot colored by expression, cluster, sample or group ID.

Usage

plotDR(x, dr = NULL, color_by = "condition")

Arguments

x

a SingleCellExperiment.

dr

character string specifying which dimension reduction to use. Should be one of reducedDimNames(x); default to the 1st available.

color_by

character string corresponding to a colData(x) column. Specifies the color coding.

Value

a ggplot object.

Author(s)

Helena Lucia Crowell

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)

library(scater)
sce <- runUMAP(sce, exprs_values = "exprs")

# color by pS6 expression, split by group
plotDR(sce, color_by = "pS6") +
  facet_wrap("condition")

# color by 8 metaclusters, split by sample
plotDR(sce, color_by = "meta8") + 
  facet_wrap("sample_id", ncol = 4)


[Package CATALYST version 1.10.3 Index]