Mice DEGs for SBGNview plot

Question

[alwayshope]

Dear all,

May I know if you have experience using the SBGNview on the mice RNA-seq data?

The manual shows the input gene.data can be a vector as used in the pathview, while when trying to run the same input of mice data to the SBGNview, it only output the blank plot, while when changing the org ="hsa" and using one of the human Reactome pathways, and similar format input vector from human data, it works fine.

Thank you very much for your kind guidance!

  sbgnview.obj <- SBGNview(
    gene.data = vector_mice2,
    gene.id.type = "entrez",sbgn.dir = "/Reactome_pathways/",sbgn.gene.id.type = "SYMBOL",
    input.sbgn = c("R-MMU-177929.sbgn"),   ### EGFR pathway from Reactome
    output.file = "EGFR_mouse",
    show.pathway.name = TRUE,
    max.gene.value = 1,
    min.gene.value = -1,
    #mid.gene.value = 0,
    node.sum = "mean",
    output.format = c("png"),

    #font.size = 2.3,
    org = "mmu",

    #text.length.factor.complex = 3,
    if.scale.compartment.font.size = TRUE,
    #node.width.adjust.factor.compartment = 0.04 
  )
  ######
  sbgnview.obj

[theodore]

Hi there, I have a couple of questions. A. I am on the same boat, I got some questions, where did you find the reactome sbgn files? B. for me when I perform input.pathways <- findPathways(org = "mmu"), I still get the hsa reactome pathways:head(paths.mmu[which(paths.mmu$sub.database == "reactome"),],1L)

head(paths.mmu[which(paths.mmu$sub.database == "reactome"),],1L)
      pathway.id                                             pathway.name sub.database
976 R-HSA-10968