| 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)