Hi all,

I found that the download.kegg() function, that is called by pathview(), returns empty empty xml for some kegg pathways. Thus, I couldn't get my data integrated in this cases. Does this happens just with my machine? Is there a way to fix it?

Please find below my session information as well as commands to reproduce the error.

 I appreciate any feedback on this.

Cheers,

Lucas

###############
 

library(pathview)

download.kegg(pathway.id="00230", species="ko") #Returns normal xml

download.kegg(pathway.id="01200", species="ko") #Returns empty xml

#Other ko returning empty xml files:
#01200,01210,01212,01220,01230

###########

Session info:

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] pathview_1.8.0       org.Hs.eg.db_3.1.2   RSQLite_1.0.0       
 [4] DBI_0.3.1            AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1  
 [7] IRanges_2.2.5        S4Vectors_0.6.1      Biobase_2.28.0      
[10] BiocGenerics_0.14.0  KEGGgraph_1.26.0     graph_1.46.0        
[13] XML_3.98-1.3        

loaded via a namespace (and not attached):
 [1] XVector_0.8.0     magrittr_1.5      zlibbioc_1.14.0   R6_2.1.0         
 [5] stringr_1.0.0     httr_1.0.0        tools_3.2.2       grid_3.2.2       
 [9] png_0.1-7         Rgraphviz_2.12.0  KEGGREST_1.8.0    stringi_0.5-5    
[13] Biostrings_2.36.1

The download.kegg() function just downloads what is available from KeGG. If the XML file is unavailable, you get an empty file. You can test this yourself. Try the link for ko00230 versus that for ko01200.
 

Hi James,

Thanks for the answer. Much appreciated! I guess there is no way to pathview function work properly for those kos with empty xml :(.

Cheers,

Lucas

Hi James,

An update.

Apparently, The KGML files for the global and overview maps (map number 01100s and 01200s) cannot be downloaded from the pathway map pages. However, they can be accessed via API, with another address,e.g. http://rest.kegg.jp/get/ko01100/kgml

I failed miserably to integrate this into the pathview code. I will get in contact with the developer of the package to see if it can be fixed for the next release.

Cheers,

Lucas