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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,
  as_points = FALSE,
  size = 1.5,
  background = NULL,
  log_pval = TRUE,
  p_cutoff = NULL,
  spots = NULL,
  spot_pval = NULL,
  title = 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.

as_points

Logical. If TRUE, draw each bin as a dot at its centroid instead of its polygon. Useful for Visium, where each bin is a single spot. Default FALSE (draw polygons).

size

Numeric. Point size when as_points = TRUE (or when background is supplied). Default 1.5.

background

A ggplot object to draw the hotspots on top of, e.g. scider::plotImage(spe) to place the H&E image behind the spots. When supplied, the hotspots are always rendered as dots (the raster background is incompatible with geom_sf coordinates), and the bins must share the background plot's coordinate frame (true for objects read by scider::readVisium()). Default NULL.

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.

spots

Integer vector or NULL. Significant spot indices to plot directly, bypassing the LR-pair lookup – e.g. a sig_spot_index entry from blisaPathway. When supplied, index/ ligand/receptor/p_cutoff are ignored and every bin is drawn as grey background with these spots coloured. Default NULL.

spot_pval

Numeric vector. P-values for spots (same length and order); required when spots is supplied.

title

Character or NULL. Plot title. Defaults to the LR pair id (or "hotspots" in spots mode). Useful to label a pathway, e.g. title = "MDK pathway".

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)
} # }