Restructure the bins of paths that share a root

sc.restruct() rebuilds the bins so that every end path starts at the root: the bins of each link path are added to the end paths it links, the bins of the root to every end path, the binned pseudotime of the later bins is shifted to follow them, and pb_counts() recomputes the pseudo-bulk counts.

Usage

sc.restruct(
  scmpObj,
  end_node_list,
  root_node,
  link_node_list,
  assay_name = "counts",
  aggregate = "sum",
  link_sep = "_links_",
  verbose = TRUE
)

Arguments

scmpObj

A ScMaSigPro object.

end_node_list

A list of the labels of the end paths.

root_node

The label of the root path.

link_node_list

A list of the labels of the link paths, the segments that some end paths share; a label holds the labels of the paths it links, separated by link_sep.

assay_name

The name of the assay of the Sparse slot that holds the counts of the cells.

aggregate

How the counts of the cells of a bin are combined: "sum" or "mean" (rounded to whole numbers).

link_sep

The separator in the labels of the link paths, matched as fixed text when the label contains it and as a regular expression otherwise, so "|" and "\\|" both work.

verbose

Whether to print progress messages.

Value

The object with the bins of every end path, from the root on, and their pseudo-bulk counts in the Dense slot.

See also

assign_paths(), which labels the root and link paths.

Other workflow steps: sc.cluster.trend(), sc.filter(), sc.p.vector(), sc.set.poly(), sc.squeeze(), sc.t.fit()

Author

Priyansh Srivastava spriyansh29@gmail.com

Examples

data("multi.lin.sce", package = "scMaSigPro")
scmp <- as_scmp(multi.lin.sce,
    additional_params = list(
        labels_exist = TRUE, exist_ptime_col = "Monocle3_Pseudotime",
        exist_path_col = "group"
    ),
    verbose = FALSE
)
scmp <- sc.squeeze(scmp)
# Three end paths, one link path shared by two of them, and the root
scmp <- sc.restruct(scmp,
    end_node_list = list("path_Y_15", "path_Y_18", "path_Y_52"),
    root_node = "root", link_node_list = list("path_Y_18|path_Y_15"),
    link_sep = "|", verbose = FALSE
)
table(cDense(scmp)$Path)
#> 
#> path_Y_15 path_Y_18 path_Y_52 
#>        23        24        19