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RunSlingshot

Source: R/RunSlingshot.R
RunSlingshot.Rd

RunSlingshot

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,
  ...,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

group.by

Name of one or more meta.data columns to group (color) cells by.

reduction

Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.

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

Random seed for reproducibility. Default is 11.

...

Additional arguments to be passed to the slingshot::slingshot function.

verbose

Whether to print the message. Default is TRUE.

See also

CellDimPlot, RunDynamicFeatures, RunDynamicEnrichment

Examples

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

# 3D lineage
pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "StandardpcaUMAP3D"
)
CellDimPlot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP",
  lineages = paste0("Lineage", 1:2),
  lineages_span = 0.1,
  lineages_trim = c(0.05, 0.95)
)