Error: Function "BanksyObject" Not Found

[melocery]

I encountered an error while running the script process_hypothalamus_merfish.R which uses the BanksyObject function. The error message is:

Error in BanksyObject(own.expr = expr.list, cell.locs = locs.list) : 
  could not find function "BanksyObject"

I searched through the GitHub repository and could not find this function. Below is the relevant section of my code:

if (USE_PROVIDED_BANKSY_OBJ){
  bank <- readRDS(file = paste0(data.dir, 'banksyObj_provided.rds'))
  
} else {
  # # Load data
  all_mfish = fread('data/merfish_all_cells.csv') # see the readme file in the data dir
  all_mfish <- all_mfish[,-c('Fos')]# remove Fos gene per Moffitt manuscript
  all_mfish = cbind(cell_ids = paste0('cell_', 1:nrow(all_mfish)), all_mfish)
  m.list = lapply(list_of_animal_IDs, function(x) all_mfish[all_mfish$Animal_ID==x,])
  expr.list <- lapply(m.list, function(x){
    expr = t(as.matrix(x[,-c(1:10)]))
    colnames(expr) <- x$cell_ids
    expr})
  locs.list <- lapply(m.list, function(x){
    df = as.data.frame(cbind(sdimx = x$Centroid_X, sdimy = x$Centroid_Y,
                             sdimz = 1000*x$Bregma))
    rownames(df) <- x$cell_ids
    df})
  names(expr.list) <- names(locs.list) <- paste0('Animal_', list_of_animal_IDs)
  
  # ------ start clustering block ---------
  bank <- BanksyObject(own.expr = expr.list, cell.locs = locs.list)
  all_mfish_by_animal_list = lapply(list_of_animal_IDs, function(x) all_mfish[Animal_ID %in% x,
                                                                              c('cell_ids',
                                                                                'Animal_ID',
                                                                                'Animal_sex',
                                                                                'Behavior',
                                                                                'Bregma',
                                                                                'Centroid_X',
                                                                                'Centroid_Y',
                                                                                'Cell_class',
                                                                                'Neuron_cluster_ID')])
  bank@meta.data = cbind(bank@meta.data, do.call(rbind, all_mfish_by_animal_list))
  
  # bank <- ComputeBanksy(bank, k_geom = k_geom)
  ram_compute_banksy = peakRAM(bank <- ComputeBanksy(bank, k_geom = k_geom))
  
  # bank <- ScaleBanksy(bank)
  ram_scale_banksy = peakRAM(
    bank <- ScaleBanksy(bank)
  )
  
  lambdas<-c(0, lambda)
  
  # bank <- Banksy:::RunBanksyPCA(bank, lambda = lambdas, npcs = npcs)
  ram_pca_banksy = peakRAM(
    bank <- Banksy:::RunBanksyPCA(bank, lambda = lambdas, npcs = npcs)
  )
  
  # bank <- Banksy:::RunBanksyUMAP(bank, lambda = lambdas, npcs = npcs, nneighbors = k_expr)
  
  ram_umap_banksy = peakRAM(
    bank <- Banksy:::RunBanksyUMAP(bank, lambda = lambdas, npcs = npcs, nneighbors = k_expr)
  )
  
  clust_major_numeric = as.numeric(factor(bank@meta.data$Cell_class))
  clust_major_names = as.character(factor(bank@meta.data$Cell_class))
  bank@meta.data = cbind(bank@meta.data, clust_major_num = clust_major_numeric)
  set.seed(42)
  ptm <- proc.time()
  # bank <- ClusterBanksy(bank, lambda = lambdas, pca = TRUE, npcs = npcs,
  #                       method = 'leiden', k.neighbors = k_expr, resolution = res)
  ram_cluster_banksy = peakRAM(
    bank <- ClusterBanksy(bank, lambda = lambdas, pca = TRUE, npcs = npcs,
                          method = 'leiden', num.cores = 8,
                          k.neighbors = k_expr, resolution = res)
  )
  time_taken = proc.time() - ptm
  print(time_taken)
  saveRDS(bank, file = paste0(data.dir, 'banksyObj_naive_', number_of_animals, '.rds'))
  # bank <- readRDS(file = paste0(data.dir, 'banksyObj_naive_run.rds'))
  # ------ end clustering block ---------
}

I suspect that the package version might be incorrect or I might be missing some additional setup steps. Could you please help me identify whether I have the wrong package version, or if there's something else I'm missing?

Thank you!

[vipulsinghal02]

Hi! All the analyses in these scripts were done using an older version of BANKSY. Try using this line to install banksy:
remotes::install_github("prabhakarlab/Banksy@main") # to install 0.1.5.

You can share your session info with us, that might be helpful in case the problem is something else..

[melocery]

After changing to version 0.1.5, the script runs smoothly. Thank you!

[vipulsinghal02]

Excellent!