Displaying the KEGG pathway image in R notebook

Question

[akansha.gitanjali]

I used the pathview package to generate images for KEGG pathways. The code below creates an image inside the folder.

Transcription <- pathview(gene.data  = genelist,
                          pathway.id = "hsa03020",
                          species    = "hsa",
                          limit      = list(gene=max(abs(genelist)), cpd=1))

But when I am trying to create an html_notebook in R, I want the images to be embedded in the notebook itself, like here: https://yulab-smu.github.io/clusterProfiler-book/chapter12.html#pathview-from-pathview-package. Instead the preview to HTML option is giving me this error:

    Transcription <- pathview(gene.data  = Rucaparib2,
                          pathway.id = "hsa03020",
                          species    = "hsa",
                          limit      = list(gene=max(abs(Rucaparib2)), cpd=1))
cannot open URL 'http://rest.kegg.jp/get/hsa03020/kgml': HTTP status was '503 Service Unavailable'

Is there any way of embedding the KEGG pathway as image in my notebook?

Answer 1

[h.mon]

The problem is not with R, R notebook, or the package pathview, the problem is the KEGG REST API is down right now. If this is permanent or temporary, I don't know - I couldn't find any information in this regard.

If you try the examples at the KEGG REST API help page (e.g. /get/cpd:C01290+gl:G00092), they are not working as well, with a strange message:

Virus/Spyware Download Blocked

Download of the virus/spyware has been blocked in accordance with company policy. Please contact your system administrator if you believe this is in error.

File name: image