Plot Spatial Co-localization — Plot

Visualizes spatial co-localization of two cell groups, genes, or metadata features in selected samples or niches.

Usage

Plot_SpatialCoLoc(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  meta_key = NULL,
  niche_key = NULL,
  group_by = NULL,
  group_use = NULL,
  features = NULL,
  feature_colnm = NULL,
  exp_thres = 1,
  col = COLOR_LIST$PALETTE_WHITE_BG,
  pt_size = 1.5
)

Arguments

STID_obj: An STID object.
loop_id: Character, sample loop identifier (default: "LoopAllSamp").
meta_key: Character, metadata key used when niche_key is NULL.
niche_key: Character, niche key used to retrieve niche cells.
group_by: Character, metadata column for group-based co-localization.
group_use: Character vector, groups to keep from group_by.
features: Character vector, feature or gene names for co-localization.
feature_colnm: Character vector, metadata columns used as features.
exp_thres: Numeric, threshold below which feature values are set to zero (default: 1).
col: Character vector, color palette (default: COLOR_LIST$PALETTE_WHITE_BG).
pt_size: Numeric, point size for spatial plots (default: 1.5).

Value

Invisibly returns NULL; spatial plots are printed.

Examples

if (FALSE) { # \dontrun{
Plot_SpatialCoLoc(
STID_obj = STID_obj,
niche_key = "niche_virulence",
group_by = "cell_type",
group_use = c("Macrophage", "T cell")
)

Plot_SpatialCoLoc(
STID_obj = STID_obj,
niche_key = "niche_virulence",
features = c("Cxcl10", "Isg15")
)
} # }