plotDR {CATALYST} | R Documentation |
Dimension reduction plot colored by expression, cluster, sample or group ID.
plotDR(x, dr = NULL, color_by = "condition")
x |
|
dr |
character string specifying which dimension reduction to use.
Should be one of |
color_by |
character string corresponding to 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 & 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)