bugfix in ResetModuleNames

Package: hdWGCNA

Title: hdWGCNA

Version: 0.2.14

Version: 0.2.15

Authors@R: c(

    person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),

           comment = c(ORCID = "0000-0002-7768-4856")),

# hdWGCNA 0.2.15 (2023-03-02)

## Added

- None

## Changes

- Bugfix to allow `ResetModuleNames` and `ResetModuleColors` to work when a grey module is not present.

# hdWGCNA 0.2.14 (2023-02-14)

## Added

- None

  combined_output <- data.frame()

  for(i in 1:length(mods)){

  	cur_mod <- mods[i]

    if(max_genes != Inf){

      cur_info <- subset(modules, module == cur_mod)

      cur_info <- cur_info[,c('gene_name', paste0('kME_', cur_mod))]

      cur_genes <- top_n(cur_info, max_genes) %>% .$gene_name %>% as.character

    } else{

      cur_genes <- subset(modules, module == cur_mod) %>% .$gene_name %>% as.character

    }

    # run the enrichment test

    enriched <- enrichR::enrichr(cur_genes, dbs)

    # collapse into one db

                         external = T) {

  if (external) {

    # first, make sure inputs are correct

    inputs = Libra:::check_inputs(

    inputs = check_inputs(

      input, 

      meta = meta,

      replicate_col = replicate_col,

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

  modules <- GetModules(seurat_obj, wgcna_name)

  MEs <- GetMEs(seurat_obj, harmonized, wgcna_name)

  genes_use <- GetWGCNAGenes(seurat_obj, wgcna_name)

  genes_use <- as.character(modules$gene_name)

  params <- GetWGCNAParams(seurat_obj, wgcna_name)

  # exclude the grey module:

  #modules <- subset(modules, module != 'grey')

  #MEs <- MEs[,colnames(MEs) != 'grey']

  if(is.null(assay)){assay <- DefaultAssay(seurat_obj)}

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

    )

    rownames(kMEs) <- genes_use

    kMEs <- as.data.frame(kMEs)

  } else{

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

    kMEs <- WGCNA::signedKME(