plotMedExprs {CATALYST} | R Documentation |
Plots median marker expressions across samples computed on arcsinh-transformed intensities.
plotMedExprs( x, k = "meta20", facet = c("antigen", "cluster_id"), group_by = "condition", shape_by = NULL )
x |
a |
k |
character string. Specifies the clustering to use.
If |
facet |
|
group_by |
character string specifying
a |
shape_by |
character string specifying
a |
a ggplot
object.
Helena Lucia Crowell
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)
# 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")