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Score cell-cell interactions from BLISA hotspots

Source: R/runCCI.R
runCCI.Rd

Generic function for scoring cell-cell interactions. Dispatches on the class of x:

  • runCCI.blisa accepts a blisa object. If CCI_scores are already present and overwrite = FALSE (the default), the object is returned unchanged. Set overwrite = TRUE with a counts_by_group to recompute and replace existing scores. If no scores exist, counts_by_group must be supplied and scores are computed and attached.

  • runCCI.default performs the raw computation given a blisa object and a counts_by_group list, returning only the scores data frame. Used internally by runCCI.blisa and blisa.default.

Usage

runCCI(x, ...)

# S3 method for class 'blisa'
runCCI(x, counts_by_group = NULL, overwrite = FALSE, ...)

# Default S3 method
runCCI(x, counts_by_group, ...)

Arguments

x

A blisa object.

...

Additional arguments passed to the relevant method.

counts_by_group

Named list of gene-by-bin sparse count matrices, one per group level (e.g. cell type). Typically the counts_by_group element of the list returned by hexBinCells when group is supplied. Names must match the group levels. Required when x$CCI_scores is NULL or when overwrite = TRUE.

overwrite

Logical. If FALSE (default) and x$CCI_scores is already populated, the object is returned unchanged. If TRUE and counts_by_group is supplied, existing scores are recomputed and replaced.

Value

See individual method documentation.

runCCI.blisa: the input blisa object with CCI_scores populated (a wide data frame – rows are "Sender->Receiver" group pairs, columns are LR pairs).

runCCI.default: a data frame with "Sender->Receiver" row names and one column per significant LR pair containing the interaction score 0.5 * log2(receiver * sender + 1).

Methods (by class)

  • runCCI(blisa): Method for a blisa object. If CCI_scores are already present and overwrite = FALSE (the default), the object is returned unchanged. Set overwrite = TRUE with a counts_by_group to recompute and replace existing scores. If no scores exist, counts_by_group must be supplied and scores are computed and attached to x$CCI_scores.

  • runCCI(default): Default method. Performs the raw CCI computation and returns only the scores data frame. Typically called internally; use runCCI.blisa to compute and attach scores to a blisa object in one step.

Examples

if (FALSE) { # \dontrun{
# Continuing from the blisa() example:
# result <- blisa(spe, bin_size = 50, group = "cell_type")

# CCI is computed automatically when group is supplied to blisa();
# access the scores directly:
head(result$CCI_scores)

# Or compute / recompute scores explicitly:
binned <- hexBinCells(
  as.data.frame(SpatialExperiment::spatialCoords(spe)),
  SummarizedExperiment::assay(spe, "counts"),
  bin_size = 50, group = spe$cell_type
)
result2 <- runCCI(result, counts_by_group = binned$counts_by_group,
                  overwrite = TRUE)
} # }