runDR {CATALYST} | R Documentation |
Wrapper around dimension reduction methods available
through scater
, with optional subsampling of cells per each sample.
runDR( x, dr = c("UMAP", "TSNE", "PCA", "MDS", "DiffusionMap"), cells = NULL, features = "type", assay = "exprs", ... )
x |
|
dr |
character string specifying which dimension reduction to use. |
cells |
single numeric specifying the maximal number of cells per sample to use for dimension reduction; NULL for all cells. |
features |
a character vector specifying which
antigens to use for dimension reduction; valid values are
|
assay |
character string specifying which assay data to use
for dimension reduction; valid values are |
... |
optional arguments for dimension reduction; passed to
|
a ggplot
object.
Helena L Crowell helena.crowell@uzh.ch
Nowicka M, Krieg C, Crowell HL, 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) # run UMAP on <= 200 cells per sample sce <- runDR(sce, features = type_markers(sce), cells = 100)