I am working on many pathways that can be found in Kegg database. Initially I tried using pathview to look at both metabolomics and transcriptomics data, then I found out specific nodes of interest could not be shown, especially when I have more than thousands of pathway to look at. By using SBGNview, it performed amazingly as what I need yet many pathway that can be found in kegg are not included in their search functions, even though the vignette mentioned it search beyond kegg and other database, for example, "dorso-ventral axis formation" of dme, ko04230. As I could not find it with function: findPathways(), I customized a SBGN file from Kegg with the following command:
SBGNview(gene.data = gene.data, org = "dme", input.sbgn = "ko04320-ortholog.sbgn", sbgn.dir = "./",output.file = "dorso.out", sbgn.gene.id.type = "KO", gene.id.type = "KO", output.formats = c("png","pdf"))
Processing pathway: ko04320-ortholog.sbgn
ko04320-ortholog.sbgn looks like a local file. Using it directly.
Using user defined pathway SBGN-ML file!!
reading SBGN-ML file for arcs info: .//ko04320-ortholog.sbgn
Rendering SBGN graph
checking graph size and create margin for color panel
parsing ports
parsing glyphs
Map language is NA
Error in if (map.language == "entity relationship") { :
missing value where TRUE/FALSE needed
Do I need to do some kind of ID mappings so that the sbgn file can recognize my gene data? Below is the screenshot of my sbgn file
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Also, please let me know if there is a way to connect this package to Kegg database, that would be the best solution of all, thank you!
2 answers
Hello greyman,
It looks like the kegg translator tool did not specify a map langauge in the sbgn file format. The map langague is necessary for SBGNview to process the input sbgn file. Also, I noticed that only few arcs were translated to sbgn from the kgml format. I would suggest using Pathview to work with pathways from kegg and maybe use a third-party tool to highlight the nodes you are interested in.
greyman,
Thanks for you interest and feedback. As you mentioned, SBGNview can highlight nodes (genes/proteins/enzymes, compounds/metabolites), edges (connections between nodes), sub-pathways or paths. It also provides extensive graphics controls on other aspects of the graphs.
https://bioconductor.org/packages/release/bioc/vignettes/SBGNview/inst/doc/SBGNview.Vignette.html#7_Updating__modifying_graphs
SBGNview does not include KEGG because it is already supported by Pathview. Your question suggests that highlighting funcitons may also be useful for KEGG pathways, We will try to include KEGG pathways in SBGNview in the near future.
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