Runnable code:
library(cola)
library(scRNAseq)
data = ReprocessedAllenData()
mat = assays(data)$rsem_tpm
mat = log2(mat + 1)
mat = adjust_matrix(mat)
anno = colData(data)[, c("driver_1_s", "dissection_s", "Core.Type", "Primary.Type", "Secondary.Type")]
anno = as.data.frame(anno)
rh = hierarchical_partition(mat, subset = 500, cores = 4, anno = anno)
saveRDS(rh, file = "ReprocessedAllen_cola_rh.rds")
cola_report(rh, output = "ReprocessedAllen_cola_rh_report", title = "cola Report for Hierarchical Partitioning - 'ReprocessedAllen'")
The HTML report is here. (generated by cola version 2.0.0, R 4.1.0.)