Closed apelin20 closed 2 years ago
Hey,
If this persists, please raise an issue with KEGGgraph.
Meanwhile, if visualization is not necessary, you may set visualize_enriched_terms=FALSE
in run_pathfindR()
and you could also visualize the enriched terms later via visualize_terms()
Hope this helps, -E
I was wondering if you could help me with this function. I first run
RA_output <- run_pathfindR(input, n_processes=8, adj_method = "fdr", p_val_threshold = 0.05, gene_sets = "KEGG", output_dir = outputdir, convert2alias = TRUE, visualize_enriched_terms = FALSE)
That completes without error. Then I run:
visualize_terms(RA_output, input_processed = TRUE, hsa_KEGG = TRUE, pin_name_path = "KEGG")
but get error:
Error in visualize_hsa_KEGG(hsa_kegg_ids = result_df$ID, input_processed = input_processed, :
`input_processed` should be a data frame
Calls: visualize_terms -> visualize_hsa_KEGG
Execution halted
Since I already did run_pathfindR, I was feeding the output to visualize_terms, but somehow I am not doing it correctly.
as the error states you should provide the processed input data frame for input_processed
. This can be achieved via input_processing ()
Thanks, that was an easy fix. Going back to KEGG pathways and KEGGgraph error. Is there any way I can download all the KEGG pathways from here for example (https://www.kegg.jp/kegg/download/Readme/README.pathway) and point pathfindR to them locally?
I'm afraid that's not possible. However, updating to the latest version of KEGGREST resolves the issue. To be clear, you don't need KEGGgraph
Thanks Ege, I got the same answer from KEGGREST - https://github.com/Bioconductor/KEGGREST/issues/12
installing through install_github("Bioconductor/KEGGREST") did the trick.
Hello,
pathfindR is failing to download KEGG pngs (sorry have to use pastebin):
https://pastebin.com/t7iv3K9j
I believe the issue is with KEGGgraph:
https://pastebin.com/d7n6syyP
Where in pathfindR can I replace the code of using KEGGgraph to download KEGG pngs with something else?
KEGGgraph_1.50.0 R ver 4.0.2 pathfindR Version: 1.6.3
Thanks, Adrian