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Spatial hotspot map for one ligand-receptor pair

Source: R/plotHotspots.R
plotHotspots.Rd

Generic function. Plots each bin coloured by significance status: empty, non-significant, or significant hotspot (continuous gradient of -log10 p-value or 1 - p-value).

Usage

plotHotspots(x, ...)

# S3 method for class 'blisa'
plotHotspots(
  x,
  index = 1,
  ligand = NULL,
  receptor = NULL,
  log_pval = TRUE,
  p_cutoff = NULL,
  ...
)

Arguments

x

A blisa object.

...

Additional arguments passed to the method.

index

Integer. Row index into LR_results selecting the ligand-receptor pair to visualise. Ignored when both ligand and receptor are supplied. Default 1 (top-ranked pair).

ligand

Character. Ligand gene symbol. When both ligand and receptor are provided the matching LR pair is located automatically and index is ignored. Must be supplied together with receptor.

receptor

Character. Receptor gene symbol. Must be supplied together with ligand.

log_pval

Logical. If TRUE (default), colour significant bins by -log10(p-value). If FALSE, use 1 - p-value.

p_cutoff

Numeric or NULL. When NULL (default), the pre-computed hotspot bins stored in the blisa object are used, reflecting the p_cutoff and High-High quadrant classification applied during blisa. When a numeric value is supplied, bins are re-defined on the fly as those with all_pval <= p_cutoff and quadrant label "High-High" (from the stored all_quadrant), giving an exact re-threshold consistent with the original classification.

Value

A ggplot object.

Methods (by class)

  • plotHotspots(blisa): Method for a blisa object.

Examples

if (FALSE) { # \dontrun{
# Continuing from the blisa() example:
# result <- blisa(spe, bin_size = 50, group = "cell_type")
plotHotspots(result, index = 1)
plotHotspots(result, index = 1, log_pval = FALSE)
} # }