This function counts inlaid/annotation composition within each cluster in a single call. It returns a dataframe with counts of inlaid types for each source cluster.
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
- clusters
Optional vector of cluster labels to process. If `NULL`, all unique clusters in `df` are used.
- 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"`.
Value
A data.frame with columns:
- cluster
The source cluster being analyzed.
- inlaid
The inlaid/annotation type.
- count
Number of spots with this inlaid type in the cluster.
- proportion
Proportion of this inlaid type among all spots in cluster.
Rows are grouped by source cluster and sorted by count within each group (descending).
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 inlaid statistics for all clusters
all_inlaids <- count_all_inlaids(df, inlaid_col = "inlaid")
#> Error in count_all_inlaids(df, inlaid_col = "inlaid"): is.data.frame(df) is not TRUE
head(all_inlaids)
#> Error: object 'all_inlaids' not found