Create a ScMaSigPro object from a SingleCellExperiment

as_scmp() creates a ScMaSigPro object from a SingleCellExperiment whose cell metadata (colData) holds a pseudotime column and a path column. To start from a count matrix and a cell table, use create_scmp(); assign_paths() and paths_from_graph() build the two columns from the output of a trajectory tool.

Usage

as_scmp(
  object,
  from = "sce",
  path_prefix = "Path",
  root_label = "root",
  ptime_col = "Pseudotime",
  path_col = path_prefix,
  verbose = TRUE,
  additional_params = list(labels_exist = FALSE)
)

Arguments

object: A SingleCellExperiment with the counts of the cells.
from: The class of object; only "sce" is supported.
path_prefix: The default of path_col, kept in the parameters.
root_label: The label of the root cells, kept in the parameters.
ptime_col: The name of the column of the cell metadata that holds the pseudotime of each cell.
path_col: The name of the column of the cell or bin metadata that holds the path label of each cell or bin.
verbose: Whether to print progress messages.
additional_params: A list: with labels_exist = TRUE, the columns exist_ptime_col and exist_path_col of the cell metadata are renamed to ptime_col and path_col.

Value

A ScMaSigPro object with the cells in the Sparse slot.

Author

Priyansh Srivastava spriyansh29@gmail.com

Examples

data("splat.sim", package = "scMaSigPro")
scmp <- as_scmp(splat.sim,
    additional_params = list(
        labels_exist = TRUE, exist_ptime_col = "Step",
        exist_path_col = "Group"
    ),
    verbose = FALSE
)
scmp
#> Class: ScMaSigProClass
#> nCells: 200
#> nFeatures: 100
#> Pseudotime Range: 1 100
#> Branching Paths: Path2, Path1