This function classifies spots within a target cluster into three layers: core, intermediate, and border. The border layer consists of spots at the cluster interface (touching other clusters). The core layer consists of spots far from any border. The intermediate layer bridges the two, with depth defined by proximity to the border.
Usage
create_cluster_layers(
df,
target_cluster,
k = 6,
max_dist = NULL,
intermediate_quantile = 0.5,
coord_cols = c("x", "y"),
cluster_col = "cluster"
)Arguments
- df
A data.frame containing at least the coordinate columns and a cluster label column.
- target_cluster
Cluster label for which to create layers.
- k
Integer. Number of nearest neighbors to consider (excluding self) when identifying border spots. Default is 6.
- max_dist
Optional numeric. Maximum Euclidean distance for neighbors. If `NULL`, no distance filtering is applied.
- intermediate_quantile
Numeric between 0 and 1. The quantile of distances to border used to define the intermediate layer threshold. Default is 0.5 (median). #' Spots with distance to border <= this quantile threshold are classified as intermediate. Use lower values (e.g., 0.33) for narrower intermediate layers, higher values (e.g., 0.75) for wider intermediate layers.
- coord_cols
Character vector of length 2 giving the coordinate column names. Default is `c("x","y")`.
- cluster_col
Character. Name of the column containing cluster labels. Default is `"cluster"`.
Value
A data.frame based on `df` filtered to contain only spots from `target_cluster`, with an additional column: - `layer`: character, one of "border", "intermediate", or "core"
Details
Layer definitions: - **Border**: Spots in the target cluster that touch at least one spot from a different cluster (kNN-based). - **Intermediate**: Non-border spots whose distance to the nearest border spot is within the `intermediate_quantile` threshold of all non-border spots. - **Core**: All remaining non-border spots that are far from the border.
The `intermediate_quantile` parameter controls the depth of the intermediate layer: - 0.33: Narrow intermediate layer (only very close to border) - 0.50: Moderate intermediate layer (median distance threshold) - 0.75: Wide intermediate layer (most non-border spots included)
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)$cluster
)
#> Error in spatialCoords(spe): could not find function "spatialCoords"
# Default: moderate depth
layers <- create_cluster_layers(df, target_cluster = 1, k = 6)
#> Error in create_cluster_layers(df, target_cluster = 1, k = 6): all(coord_cols %in% colnames(df)) is not TRUE
table(layers$layer)
#> Error: object 'layers' not found
# Narrow intermediate layer
layers_narrow <- create_cluster_layers(df, target_cluster = 1, k = 6,
intermediate_quantile = 0.33)
#> Error in create_cluster_layers(df, target_cluster = 1, k = 6, intermediate_quantile = 0.33): all(coord_cols %in% colnames(df)) is not TRUE
table(layers_narrow$layer)
#> Error: object 'layers_narrow' not found