R/cluster.R
connectClusters.Rd
Relabel cluster labels across parameter runs to maximise their similarity.
connectClusters(se, map_to = NULL, verbose = TRUE)
A SpatialExperiment / SingleCellExperiment / SummarizedExperiment
object with 'connected' cluster labels in colData(se)
.
data(rings)
spe <- computeBanksy(rings, assay_name = "counts", M = 1, k_geom = c(15, 30))
#> Computing neighbors...
#> Spatial mode is kNN_median
#> Parameters: k_geom=15
#> Done
#> Computing neighbors...
#> Spatial mode is kNN_median
#> Parameters: k_geom=30
#> Done
#> Done
#> Centering
#> Done
spe <- runBanksyPCA(spe, M = 1, lambda = c(0, 0.2), npcs = 20)
spe <- clusterBanksy(spe, M = 1, lambda = c(0, 0.2), resolution = 1)
spe <- connectClusters(spe)
#> clust_M1_lam0_k50_res1 --> cluster
#> clust_M1_lam0.2_k50_res1 --> clust_M1_lam0_k50_res1