Add trajectory information to SpatialExperiment colData — add_trajectories_to

This function takes trajectory results (e.g., from [build_similar_trajectories()]) and adds trajectory metadata to the colData of a SpatialExperiment object.

Usage

add_trajectories_to_spe(spe, trajectory = NULL, erase = FALSE)

Arguments

spe: A SpatialExperiment object from which the trajectory dataframes were derived.
trajectory: A data.frame of trajectory spots. Expected output from [build_similar_trajectories()]. Expected columns: spot_id, trajectory_id, offset, pos_on_seg, dist_to_seg.
erase: Logical. If `TRUE`, erase pre-existing trajectory columns before adding new ones. If `FALSE` (default), issue a warning if columns already exist and skip adding them.

Value

The SpatialExperiment object with updated colData.

Details

The `trajectories` parameter must be provided and contain at least one row.

The following columns are added: - `trajectory_id`: character, identifier for each trajectory (e.g., "main", "left_1", "right_2") - `offset`: numeric, the offset distance used to build each trajectory line - `pos_on_seg`: numeric in [0, 1], the position along the trajectory - `dist_to_seg`: numeric, the distance to the original segment

Examples

data("visiumHD_16um_simulated_spe", package = "Battlefield")
spe <- visiumHD_16um_simulated_spe
df <- data.frame(
  spot_id = colnames(spe),
  x = spatialCoords(spe)[, 1],
  y = spatialCoords(spe)[, 2],
  cluster = colData(spe)$cluster
)
#> Error in spatialCoords(spe): could not find function "spatialCoords"
centroids <- compute_centroids(df)
#> Error in model.frame.default(formula = cbind(x, y) ~ cluster, data = df): 'data' must be a data.frame, environment, or list
A <- centroids[centroids$cluster == 1, c("x", "y")]
#> Error: object 'centroids' not found
B <- centroids[centroids$cluster == 3, c("x", "y")]
#> Error: object 'centroids' not found
trajs <- build_similar_trajectories(df, A, B, top_n = 10, n_extra = 1, side =
"both")
#> Error in estimate_spot_spacing(df): all(c("x", "y") %in% names(df)) is not TRUE
spe <- add_trajectories_to_spe(spe, trajectory = trajs)
#> Error: object 'trajs' not found