Skip to contents

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, weighted = TRUE, ...)

# Default S3 method
runCCI(x, counts_by_group, weighted = TRUE, ...)

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.

weighted

Logical. If TRUE (default), the ligand count of each sender group is the sum over hotspots \(h\) of its spatially weighted ligand counts around \(h\), \(\sum_h \sum_j w_{hj} L_j\), using the same neighbours and row-standardised spatial weights as the bivariate Moran's I test. This is the sum of the local ligand terms used by plotCCIspatial. If FALSE, ligand counts are summed without weights over the hotspot bins and their neighbours, each bin counted once.

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)
} # }