ModuleConnectivity

  harmonized=TRUE,

  assay = NULL,

  slot = NULL,

  use_metacells = FALSE,

  group.by = NULL,

  group_name = NULL,

  wgcna_name = NULL,

  ...

){

  # set as active assay if wgcna_name is not given

  if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

  if(use_metacells){

    warning('use_metacells option is not implemented yet.')

  }

  # get module df, wgcna genes, and wgcna params:

  modules <- GetModules(seurat_obj, wgcna_name)

  MEs <- GetMEs(seurat_obj, harmonized, wgcna_name)

  print(head(genes_use))

  print(class(GetAssayData(seurat_obj, assay=assay, slot=slot)))

  datExpr <- t(GetAssayData(

  if(!is.null(group.by)){

    cells.use <- seurat_obj@meta.data %>% subset(get(group.by) == group_name) %>% colnames

  } else{

    cells.use <- colnames(seurat_obj)

  }

  # get expression data:

  exp_mat <- GetAssayData(

    seurat_obj,

    assay=assay,

    slot=slot

  ))[,genes_use]

  )[genes_use,cells.use]

  datExpr <- t(as.matrix(exp_mat))

  print('datExpr')

  print(dim(datExpr))