Visualize the landmark-trajectory relevance and the sample-level cell density

SampleLevelDimPlot(
  object = NULL,
  sample.obj = NULL,
  rename.sample = NULL,
  weighted.nn.name = "weighted.nn",
  landmark.assay.name = "LANDMARK",
  features.to.test = NULL,
  order = TRUE,
  pt.size = 0.5,
  alpha = 0.8,
  ncol = NULL,
  return.seurat.obj = TRUE,
  k.nn = 20,
  min.dist = 0.3,
  ...
)

Arguments

object: Seurat object
sample.obj: Sample-level Seurat object
rename.sample: Optional sample renaming
weighted.nn.name: Name of weighted NN object
landmark.assay.name: Name of landmark assay
features.to.test: Features to test for correlation
order: Whether to order points
pt.size: Point size
alpha: Point transparency
ncol: Number of columns
return.seurat.obj: Whether to return Seurat object
k.nn: Number of nearest neighbors
min.dist: Minimum distance for UMAP
...: Additional arguments

Value

List containing plots and optionally landmark object