Calculate pathogen tracking across samples — CalSampPathoTrack • STID

Analyzes pathogen distribution across temporal or comparative samples, infers dissemination networks, and visualizes pathogen spread patterns.

Usage

CalSampPathoTrack(
  STID_obj = NULL,
  loop_id = NULL,
  samp_grp_index = FALSE,
  meta_key = NULL,
  niche_key = NULL,
  group_by = NULL,
  pos_colnm = NULL,
  neg_value = "neg",
  col = COLOR_LIST[["PALETTE_WHITE_BG"]],
  return_data = FALSE,
  grp_nm = NULL,
  dir_nm = "M4_CalSampPathoTrack"
)

Arguments

STID_obj: A STID object
loop_id: Character, multi-sample analysis identifier
samp_grp_index: Logical, whether to group by sample groups (default: FALSE)
meta_key: Character, metadata key for retrieving cell data
niche_key: Character, niche key for filtering niche cells (optional)
group_by: Character, column name for cell type grouping
pos_colnm: Character, column name containing positive spot labels
neg_value: Character, value indicating negative spots (default: "neg")
col: Character vector, color palette for cell types
return_data: Logical, whether to return results (default: FALSE)
grp_nm: Character, group name for output (default: NULL, uses timestamp)
dir_nm: Character, directory name for output (default: "M4_CalSampPathoTrack")

Value

If return_data = TRUE, returns a list containing:

pathogen_data: Pathogen-positive cell counts and ratios per time point
pathogen_wide: Wide format pathogen ratio matrix
region_summary: Peak time and total burden per cell type
edges_df: Inferred dissemination network edges
spatiotemporal_edges: Time-resolved transition edges

Details

The function performs three types of analyses:

Temporal trend analysis of pathogen-positive cell type composition
Peak-based dissemination network inference (which cell types seed others)
Transition-based spatiotemporal mapping of pathogen spread

Examples

if (FALSE) { # \dontrun{
# Track pathogen spread across time points
results <- CalSampPathoTrack(
  STID_obj = stid_object,
  loop_id = "infection_series",
  group_by = "cell_type",
  pos_colnm = "Label_pathogen"
)
} # }