BUG | do_EnrichmentHeatmap | Undefined columns selected when providing named lists with dashes on the names.

[AlexisFon]

Hi,

I encountered n issue when running "SCpubr::do_EnrichmentHeatmap".

Here is the code :

Macro_Subtypes = list(
  "IFN-TAMs" = c("CCL2", "CCL8", "CXCL9", "CXCL10", "CXCL11", "IFITM1", "ISG15"),
  "Infla-TAMs" = c("CCL3", "CCL4", "CCL20", "CCL3L1", "CCL4L2", "CXCL1", "CXCL2", "CXCL3", "CXCL5", "CXCL8", "GOS2"))

SCpubr::do_EnrichmentHeatmap(AllMacroClean, input_gene_list = Macro_Subtypes, use_viridis = T, viridis.palette = "C", legend.position = "right", flip = F)
AllMacroClean being a Seurat Object
![image](https://github.com/enblacar/SCpubr/assets/141238205/22268def-9e30-43bb-82d2-9085102fd7cd)

I have the following error :
Error in [.data.frame(sample@meta.data, , col_name) :
undefined columns selected
In addition: Warning message:
! Found dashes (-) in the name of the gene sets provided. Replacing them with dots (.) to avoid conflicts when generating the Seurat assay.

It worked before, but not anymore, and I don't understand what I have to change. Does anyone could help me ?

Alexis

[enblacar]

Hi @AlexisFon,

Thanks for using my package!

It seems a problem with the names of the list. Dashes are particularly problematic as they transform into dots when computing enrichment scores. To try to fix it, I also change them to retrieve the enrichment score columns from the metadata afterwards, but apparently, something went wrong along the way.

• Which version of SCpubr are you using?
• Can you try to remove any special characters from your names. I.E: INF-TAMs --> INFTAMs and Infla-TAMs --> InflaTAMs.

Let me know if the issue still persists after trying that!

Best,
Enrique

[enblacar]

Hi @AlexisFon,

Closing this issue for now. Feel free to reopen it in case the tips above did not help!

Best,
Enrique