plotMedExprs {CATALYST}R Documentation

Plot median expressions

Description

Plots median marker expressions across samples computed on arcsinh-transformed intensities.

Usage

plotMedExprs(
  x,
  k = "meta20",
  facet = c("antigen", "cluster_id"),
  group_by = "condition",
  shape_by = NULL
)

Arguments

x

a SingleCellExperiment{SingleCellExperiment}.

k

character string. Specifies the clustering to use. If facet = "antigen", this argument will be ignored.

facet

"antigen" or "cluster_id". Note that the latter requires having run cluster.

group_by

character string specifying a colData(x) column to group samples by.

shape_by

character string specifying a colData(x) column to shape samples by.

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
data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)

# plot median expressions
plotMedExprs(sce, shape_by = "patient_id")

# run clustering
sce <- cluster(sce)

# plot median expressions across clusters
plotMedExprs(sce, facet = "cluster_id", k = "meta8")


[Package CATALYST version 1.10.3 Index]