This function counts the composition of an inlaid/annotation column within a target source cluster. Unlike [count_neighborhood()], this counts types *inside* the source cluster itself, not around it.
Arguments
- df
A data.frame containing at least the columns `x`, `y`, cluster identifier 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 analyze inlaid composition for.
- inlaid_col
Character. Name of the column containing inlaid/annotation values. Default is `"cluster"` (to analyze cluster composition within another grouping).
- cluster_col
Character. Name of the column containing cluster assignments. Default is `"cluster"`.
Value
A data.frame with columns:
- inlaid
Inlaid/annotation value.
- count
Number of spots with this inlaid type in the cluster.
- proportion
Proportion of this inlaid type among all spots in cluster.
Rows are sorted by count in descending order.
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"
# Count inlaid types within cluster 1
inlaid_counts <- count_inlaid(df, cluster = 1, inlaid_col = "inlaid")
#> Error in count_inlaid(df, cluster = 1, inlaid_col = "inlaid"): is.data.frame(df) is not TRUE
inlaid_counts
#> Error: object 'inlaid_counts' not found