RunSlingshot: RunSlingshot

In zh542370159/SCP: Single Cell Pipeline

RunSlingshot

Description

Runs the Slingshot algorithm on a Seurat object.

Usage

RunSlingshot(
  srt,
  group.by,
  reduction = NULL,
  dims = NULL,
  start = NULL,
  end = NULL,
  prefix = NULL,
  reverse = FALSE,
  align_start = FALSE,
  show_plot = TRUE,
  lineage_palette = "Dark2",
  seed = 11,
  ...
)

Arguments

srt	A Seurat object.
group.by	The variable to group the cells by.
reduction	The reduction technique to use for dimensionality reduction. Default is NULL, which uses the default reduction for the Seurat object.
dims	The dimensions to use for the Slingshot algorithm. Default is NULL, which uses first two dimensions.
start	The starting group for the Slingshot algorithm. Default is NULL.
end	The ending group for the Slingshot algorithm. Default is NULL.
prefix	The prefix to add to the column names of the resulting pseudotime variable. Default is NULL.
reverse	Logical value indicating whether to reverse the pseudotime variable. Default is FALSE.
align_start	Logical value indicating whether to align the starting pseudotime values at the maximum pseudotime. Default is FALSE.
show_plot	Logical value indicating whether to show the dimensionality plot. Default is TRUE.
lineage_palette	The color palette to use for the lineages in the plot. Default is "Dark2".
seed	The random seed to use for reproducibility. Default is 11.
...	Additional arguments to be passed to the slingshot function.

See Also

CellDimPlot RunDynamicFeatures

Examples

data("pancreas_sub")
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP")
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "PCA", dims = 1:10)
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:2), lineages_span = 0.1)

# 3D lineage
pancreas_sub <- Standard_SCP(pancreas_sub)
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1, lineages_trim = c(0.05, 0.95))

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.