ModuleTraitCorrelation stops with error: 'group.by variable must be a factor in the seurat object metadata.'

[jopeptid]

I think the issue is related to the fact that the factor status is checked too early in the ModuleTraitCorrelation function.

ModuleTraitCorrelation <- function(
  seurat_obj,
  traits,
  group.by = NULL,
  features = 'hMEs',
  cor_method = 'pearson',
  subset_by = NULL,
  subset_groups = NULL,
  wgcna_name = NULL,
  ...
){

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

  # get MEs, module data from seurat object
  if(features == 'hMEs'){
    MEs <- GetMEs(seurat_obj, TRUE, wgcna_name)
  } else if(features == 'MEs'){
    MEs <- GetMEs(seurat_obj, FALSE, wgcna_name)
  } else if(features == 'scores'){
    MEs <- GetModuleScores(seurat_obj, wgcna_name)
  } else{
    stop('Invalid feature selection. Valid choices: hMEs, MEs, scores, average')
  }

  if(!is.factor(group.by)){
    stop('group.by variable must be a factor in the seurat object metadata.')
  }