NEWS

blisa 1.0.3 (2026-10-30)

New argument weighted in plotCCIspatial(). The ligand contribution of each sender cell type at a hotspot is now the spatially weighted sum over its neighbours.
New argument weighted in runCCI(). The global ligand count of each sender group is now the sum over hotspots of the local weighted ligand counts used by plotCCIspatial().

Added functionality for visium data
New function blisaPathway() for summarizing blisa results at the pathway level
Added a new element level to the blisa object class, specifying whether the results are lr level or pathway level
plotLRrank() and plotHotspots() not works for pathway level results

New argument platform in blisa to handle xenium and visium
New argument as_points in plotHotspots() to plot dots instead of hexagons
New argument size in plotHotspots() to change the size of the dots
New argument background in plotHotspots() to add background image (e.g., H&E)

blisa() now uses the fastLISA C/OpenMP backend by default (fast = TRUE) for the bivariate local Moran's I computation. fastLISA moved from Suggests to Imports. Results are statistically equivalent to the previous spdep::localmoran_bv backend but not bit-identical (different RNG).
New min_total_counts argument to blisa() and hexBinCells() drops bins whose total counts (summed over all genes) fall below the threshold during binning. Default 10.
New verbose argument (default FALSE) to blisa() and hexBinCells() gates progress messages; blisa() also shows a progress bar over the ligand-receptor pairs in interactive sessions.
New lr_pairs argument to plotCCI() selects specific ligand-receptor pairs to display, overriding top_lr.
New main argument to plotCCI(), plotCCILR(), and plotCCIsummary() adds a title above the heatmap.

LR_results row names are now informative IDs built from the ligand/receptor symbols, with subunits joined by | and the two sides by _ (e.g. TGFB1_TGFBR2|TGFBR1). The original CellChatDB interaction_name is retained in a new interaction_name column.
plotCCIspatial() now handles multi-subunit ligand/receptor complexes (previously errored with subscript out of bounds).
plotHotspots(), plotCCIspatial(), and plotCCILR() now match the ligand/receptor arguments by subunit set, independent of order, separator (,, _, |), and whitespace.

Added fast = TRUE option to blisa() which uses fastLISA::local_moran_bv (C/OpenMP backend) instead of spdep::localmoran_bv for the bivariate local Moran's I computation. Default behaviour unchanged.
New cpu_threads argument controlling parallelism when fast = TRUE.