UMAP3Dcubes: UMAP3Dcubes

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

UMAP3Dcubes

Description

UMAP with 3D cubes.

Usage

UMAP3Dcubes(
  obj = combined.obj,
  n_bin = 10,
  plot = FALSE,
  save.plot = FALSE,
  reduction = c("umap", "pca", "tsne")[1],
  ident = Seurat.utils::GetClusteringRuns(obj)[1],
  PCA_dim = 50
)

Arguments

obj	Seurat single cell object, Default: combined.obj
n_bin	Number of bins, Default: 10
plot	Plot results? Default: FALSE
save.plot	Save plot into a file. Default: FALSE
reduction	Which dim. reduction to use? Default: c("umap", "pca", "tsne")1
ident	Identity (metadata), Default: Seurat.utils::GetClusteringRuns(obj)1
PCA_dim	PCA dimensions, Default: 50

See Also

RunUMAP, RunTSNE, reexports binning modal reexports open3d, shade3d, matrices, cube3d, rglwidget saveWidget

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.