Error in term_gene_heatmap function

[safrikDut]

Hi!
Thanks a lot for answering my last question! Now I have an error in the term_gene_heatmap function that I cannot figure out the source of error:

term_gene_heatmap <- term_gene_heatmap(result_df = final_res,

•                                    genes_df = DMSO_mock, 
  

•                                    num_terms = 20,
  

•                                    use_description = TRUE,
  

•                                    pin_name_path = "STRING",
  

•                                    low = "red",
  

•                                    mid = "black",
  

•                                    high = "green")
  

Error in input_testing(genes_df) : p values must all be numeric

I am using the same input file in genes_df as for run_PathfindR. I have also run enrichment_chart functions without any trouble.
Any help will be very much appreciated!

Thanks!

[egeulgen]

Hey @safrikDut,

Would you mind sharing the DMSO_mock and final_res as RDS files so that I can try to replicate the issue?

[safrikDut]

Hi!
Of course!
files.zip

Thanks!

[egeulgen]

Hello again @safrikDut,
The issue was that DMSO_mock is a tibble (tbl_df), changing it into a regular data frame via as.data.frame(DMSO_mock) resolves the issue.
Another comment: you should not storing the heatmap object in a variable called term_gene_heatmap as this will override the function and you cannot use the function afterwards, I suggest simply using g.

PS I will probably implement a workaround so that pathfindR works with tibbles as well.