RA_outpu error

[Shivani8898]

Hi,
I am using PathfindR for pathway enrichrichment(KEGG).
No wi am facing problem from last 2 weeks earler it was fine but i don't understand what is the problem now.
one time it is running properly another time no RA_output.
Can you please help me with that.
I tried everthing from shutdown to reinstalling R. Also, the default version of PathfindR is showing error.
This is what I get:

There is already a directory named "pathfindR_Results".
Writing the result to "pathfindR_Results(18)" not to overwrite any previous results.

Testing input

The input looks OK

Processing input. Converting gene symbols,

      if necessary (and if human gene symbols provided)

Number of genes provided in input: 9066
Number of genes in input after p-value filtering: 9066
pathfindR cannot handle p values < 1e-13. These were changed to 1e-13
Could not find any interactions for 1061 (11.7%) genes in the PIN
Final number of genes in input: 8005

Performing Active Subnetwork Search and Enrichment

Processing the enrichment results over all iterations

Annotating involved genes and visualizing enriched terms

Downloading pathway diagrams of 236 KEGG pathways

|=================== | 18%The file /var/folders/k3/2bypsbdn7mgb7n3gt5q6jhhc0000gn/T//RtmpXI6Jhu/file33745a3de0 seems not to be a valid KGML file

Detailed error messages fromXML::xmlTreeParse:
Error: 1: Couldn't find end of Start Tag rela line 1374
2: Premature end of data in tag pathway line 4

View(RA_output6)
Error in View : object 'RA_output6' not found

[egeulgen]

This seems to be an issue with obtaining the KEGG pathways? Which version of pathfindR are you using? I suspect updating to the latest version (along with updating the dependencies) should resolve the issue as there were issues with KEGGREST before

[Shivani8898]

Hi, actually i am using the latest version(1.6.4)

[egeulgen]

what version of KEGGREST are you using?

[Shivani8898]

kEGGREST VERSON-1.36.3

[egeulgen]

as this seems to be an issue with the visualization KEGG pathways, I will suggest running without visualization and performing visualization separately:

out_df <- run_pathfindR(in_df, visualize_enriched_terms = FALSE)
visualize_terms(out_df, input_processing(in_df))

The KGML file (basically XML) seems to be corrupt for some reason. From the percentage (18%), the problematic term seems to be number 42 (236 * 0.18), I would specifically check that:

visualize_terms(out_df[42, ], input_processing(in_df))

However, I suspect that this might be due to a connection issue or (more likely) there might be a request limitation for the KEGG REST API that I'm not aware of.

In summary, I'd suggest running run_pathfindR() with visualize_enriched_terms = FALSE to obtain the actual enrichment results and try to debug the visualization issue separately

[Shivani8898]

Thank you so much, this worked.

[Shivani8898]

Hello,
Thanks for your help in resolving the error.
I have another question related to the term gene graph. I wanted to know how can I decrease the node size so that all the terms can be fitted.
I used the following codes and got this warning message.
term_gene_graph(result_df = RA_output1, use_description = TRUE)
1: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
2: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
3: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps
4: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps

[egeulgen]

Hello,

You can change the node sizes as follows:

g <- term_gene_graph(RA_output)
g <- g + ggplot2::scale_size(range = c(2, 5), name = "# genes") # depending on your choice (when node_size == "num_genes")
g <- g + ggplot2::scale_size(range = c(2, 5), name = "-log10(p)") # depending on your choice (when node_size == "p_val")
g