ProjectModules not flexible to user-defined modules

[zvittorio]

Hello!

First of all, congrats on the amazing package, really!
I was trying to project WGCNA modules that were laying around in the lab from past experiments onto a recent scRNA-seq dataset.
The modules were saved as a text file with each row containing the gene name and the module assignment. We wanted to use hdWGCNA::ProjectModules to score their activities on scRNA-seq data and I used the following code:

library(Seurat)
library(hdWGCNA)

seurObj <- readRDS("Seurat.rds")

mods <- read.table('bulk_modules.txt', 
                      header = F, 
                      sep = "\t")

colnames(mods) <- c("gene_name", "module")
mods$color <- "grey" # just to fill the column

seurObj <- ProjectModules(
  seurat_obj = seurObj,
  modules = mods,
  seurat_ref = NULL,
  wgcna_name = "hdWGCNA",
  wgcna_name_proj = 'Modules_consensus')

Now, based on the documentation, ProjectModules can also work with a user-defined table of modules bypassing the argument seurat_ref. However, I was getting the following error:

Error in seurat_obj@misc : 
  no applicable method for `@` applied to an object of class "NULL"

Which seems to be coming from CheckWGCNAName at line 38.
For this reason I created a pull request #405 for ProjectModules where:

• seurat_ref has a default value of NULL
• seurat_ref is checked with CheckWGCNAName only when different than NULL
• function stops if both seurat_ref and modules are NULL

It works on my end, and the classical behavior (with both seurat_obj and seurat_ref being provided) should not changed.
Let me know if I misunderstood anything!

Vittorio

[smorabit]

Hi,

The latest update of hdWGCNA should resolve this issue, please let me know if you have the chance to test it.