This function retrieves all spots from a source cluster along with their inlaid/annotation values. Unlike [get_neighborhood_spots()], this returns spots *inside* the source cluster itself, not around it.
Usage
get_inlaid_spots(
df,
cluster,
inlaid_col = "cluster",
cluster_col = "cluster",
coords = c("x", "y")
)Arguments
- df
A data.frame containing at least the columns `x`, `y`, cluster identifier column, inlaid column, and `spot_id`. - `x`, `y`: numeric coordinates of spots - cluster column (name specified by `cluster_col`): cluster assignment for each spot - inlaid column (name specified by `inlaid_col`): inlaid/annotation for each spot - `spot_id`: unique identifier for each spot
- cluster
The cluster label to retrieve inlaid spots for.
- inlaid_col
Character. Name of the column containing inlaid/annotation values. Default is `"cluster"`.
- cluster_col
Character. Name of the column containing cluster assignments. Default is `"cluster"`.
- coords
Character vector of length 2 giving the coordinate column names. Default is `c("x", "y")`.
Value
A data.frame with columns:
- spot_id
Unique spot identifier.
- x
X coordinate.
- y
Y coordinate.
- inlaid
Inlaid/annotation value.
- cluster
The source cluster being analyzed.
- is_inlaid
Logical, always TRUE for returned rows.
Rows are sorted by inlaid and spot_id.
Examples
data("visium_simulated_spe", package = "Battlefield")
spe <- visium_simulated_spe
df <- data.frame(
spot_id = colnames(spe),
x = spatialCoords(spe)[, 1],
y = spatialCoords(spe)[, 2],
cluster = colData(spe)$cluster,
inlaid = sample(paste0("type_", 1:3), length(colnames(spe)), replace = TRUE)
)
#> Error in spatialCoords(spe): could not find function "spatialCoords"
# Get all inlaid spots within cluster 1
inlaid_spots <- get_inlaid_spots(df, cluster = 1, inlaid_col = "inlaid")
#> Error in get_inlaid_spots(df, cluster = 1, inlaid_col = "inlaid"): is.data.frame(df) is not TRUE
head(inlaid_spots)
#> Error: object 'inlaid_spots' not found