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Aggregate BLISA hotspots to the pathway level

Source: R/blisaPathway.R
blisaPathway.Rd

Rolls up per-ligand-receptor (LR) pair BLISA hotspot results to the signalling pathway level, grouping LR pairs by a pathway annotation column (e.g. CellChatDB's pathway_name). For each pathway it returns the spots that are hotspots for the pathway, a per-spot pathway p-value, and the LR pair driving each spot.

Usage

blisaPathway(
  x,
  method = c("minP", "simes", "fisher"),
  pathway_col = "pathway_name",
  p_cutoff = 0.05,
  p_adjust = c("none", "BH")
)

Arguments

x

A blisa object (or its LR_results data frame).

method

Character. Per-spot combination: "minP" (default, the original behaviour), "simes", or "fisher".

pathway_col

Character. Column of LR_results holding the pathway label. Default "pathway_name" (CellChatDB). Rows with NA are dropped.

p_cutoff

Numeric. Significance threshold for "simes"/ "fisher". Default 0.05. Ignored for "minP".

p_adjust

Character. Multiple-testing adjustment across spots for "simes"/"fisher": "none" (default) or "BH". Ignored for "minP".

Value

A blisa object whose LR_results slot is the pathway-level table (one row per pathway, row names = pathway, ordered by sig_numbers descending), so the standard blisa methods work directly (plotHotspots, plotLRrank, print). The bins and spatial_weights slots are carried over from x (when it is a blisa object); CCI_scores is NULL. The LR_results columns are:

sig_numbers

Number of pathway hotspot spots.

n_LR_pairs

Number of LR pairs annotated to the pathway.

sig_index

List column: the hotspot spot indices.

sig_pval

List column: the per-spot pathway p-values.

LR_pairs

List column: all LR pair IDs in the pathway.

top_LR_pair

List column: per spot, the LR pair(s) with the smallest contributing p-value.

Details

The per-spot pathway p-value is computed by one of three methods:

"minP"

The union of each LR pair's significant hotspot spots, with the minimum p-value per spot. p_cutoff and p_adjust are ignored.
"simes"

Per-spot Simes combination across all LR pairs in the pathway, using the full per-spot p-values (all_pval) restricted to the High-High co-expression direction. Non-High-High/untested contributions are set to 1.

"fisher"

As "simes" but Fisher's method.

For "simes"/"fisher", a spot is a pathway hotspot when its combined p-value is \(\le\) p_cutoff (after optional p_adjust).

See also

blisa

Examples

if (FALSE) { # \dontrun{
res <- blisa(spe, platform = "visium")
blisaPathway(res)                          # min-P (original behaviour)
blisaPathway(res, method = "simes", p_adjust = "BH")
} # }