compareClusters: Compare cluster outputs based on various clustering...
In prabhakarlab/Banksy: Spatial transcriptomic clustering

compareClusters

R Documentation

Compare cluster outputs based on various clustering comparison measures.

Description

Compare cluster outputs based on various clustering comparison measures.

Usage

compareClusters(
  se,
  func = c("ARI", "AMI", "MARI", "MARIraw", "RI", "NID", "NMI", "NVI"),
  digits = 3
)

Arguments

`se`	A `SpatialExperiment`, `SingleCellExperiment` or `SummarizedExperiment` object with cluster labels in `colData(se)`.
`func`	A string scalar specifying what clustering comparison measure to compute. See `?aricode` for more information.
`digits`	An integer scalar specifying the number of digits to round to.

Value

A matrix of cluster comparison measures.

Examples

data(rings)
spe <- computeBanksy(rings, assay_name = "counts", M = 1, k_geom = c(15, 30))
spe <- runBanksyPCA(spe, M = 1, lambda = 0.2, npcs = 20)
spe <- clusterBanksy(spe, M = 1, lambda = 0.2, resolution = c(0.1, 1))
spe <- connectClusters(spe)
compareClusters(spe)

prabhakarlab/Banksy documentation built on July 31, 2024, 7:37 p.m.