connectClusters: Relabel cluster labels across parameter runs to maximise...
In prabhakarlab/Banksy: Spatial transcriptomic clustering

connectClusters

R Documentation

Relabel cluster labels across parameter runs to maximise their similarity.

Description

Relabel cluster labels across parameter runs to maximise their similarity.

Usage

connectClusters(se, map_to = NULL, verbose = TRUE)

Arguments

`se`	A `SpatialExperiment`, `SingleCellExperiment` or `SummarizedExperiment` object with cluster labels in `colData(se)`.
`map_to`	A string scalar specify a cluster to map to.
`verbose`	A logical scalar specifying verbosity.

Value

A SpatialExperiment / SingleCellExperiment / SummarizedExperiment object with 'connected' cluster labels in colData(se).

Examples

data(rings)
spe <- computeBanksy(rings, assay_name = "counts", M = 1, k_geom = c(15, 30))
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)

prabhakarlab/Banksy documentation built on April 11, 2024, 2:45 p.m.