R version 4.4.0 alpha (2024-04-07 r86351 ucrt)
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(WayFindR)
> xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
> gr <- GPMLtoIgraph(xmlfile)
> cyc <- findCycles(gr)
> cyc
[[1]]
      dbe54 c0520 b2305 c7b3c b3356 ef7f5 ceb96 a2d31 
    2    27    15     8    18    52    30    23     2 

[[2]]
      dbe54 c0520 b2305 b3356 ef7f5 ceb96 a2d31 
    2    27    15     8    52    30    23     2 

[[3]]
      c7b3c b2305 
    8    18     8 

[[4]]
      c7b3c b3356 d51fd c0520 b2305 
    8    18    52    53    15     8 

[[5]]
      b3356 d51fd c0520 b2305 
    8    52    53    15     8 

> lapply(cyc, interpretCycle, graph = gr)
[[1]]
           genes          arrows
1           PI3K mim-stimulation
2           PDK1 mim-stimulation
3           AKT1  mim-inhibition
4          FoxO  mim-stimulation
5          MAFbx  mim-inhibition
6 mTORC1 complex mim-stimulation
7            S6K  mim-inhibition
8           IRS1 mim-stimulation

[[2]]
           genes          arrows
1           PI3K mim-stimulation
2           PDK1 mim-stimulation
3           AKT1  mim-inhibition
4          FoxO   mim-inhibition
5 mTORC1 complex mim-stimulation
6            S6K  mim-inhibition
7           IRS1 mim-stimulation

[[3]]
  genes          arrows
1 FoxO  mim-stimulation
2 MAFbx mim-stimulation

[[4]]
           genes          arrows
1          FoxO  mim-stimulation
2          MAFbx  mim-inhibition
3 mTORC1 complex  mim-inhibition
4         Group1  mim-inhibition
5           AKT1  mim-inhibition

[[5]]
           genes         arrows
1          FoxO  mim-inhibition
2 mTORC1 complex mim-inhibition
3         Group1 mim-inhibition
4           AKT1 mim-inhibition

> 
> S <- WayFindR:::cycleSubgraph(gr, cyc)
> #set.seed(13579)
> #L <- igraph::layout_with_graphopt(G)
> #plot(G, layout=L)
> 
> proc.time()
   user  system elapsed 
   0.43    0.10    0.53