How to disable module, enzyme, and gene names in the network? #24

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1. SergiPicart commented on Mar 5, 2023

   

   SergiPicart

   on Mar 5, 2023

   Contributor

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   Dear Dong,

   Please see if the code below helps. The original publication figure had small modifications with a graphical editor (e.g. putting a white background behind node labels for better readability) but you can tweak the plotting to hide node labels, change colours, etc

   Let me know if that helps
   Sergi

   # example on how to customise the plotting attributes of the sub-graph
   library(igraph)
   library(FELLA)
   
   data("FELLA.sample")
   data("input.sample")
   
   myAnalysis <- enrich(
     compounds = input.sample, 
     method = "diffusion", 
     approx = "normality", 
     data = FELLA.sample)
   
   # default FELLA plotting
   plot(myAnalysis, method = "diffusion", data = FELLA.sample)
   
   # export the graph
   g <- generateResultsGraph(object = myAnalysis, data = FELLA.sample)
   
   # again, default plotting
   plotGraph(g)
   
   # custom plotting
   # currently there is no way to get the default parameters for the graph 
   # and change them - would be a nice improvement to allow it
   # you can still find them by printing FELLA's plotting function
   print(FELLA::plotGraph)
   
   # see ?igraph.plotting for a list of options
   # Example customised parameters
   v.size <- c(
     "1" = 10,
     "2" = 6,
     "3" = 5,
     "4" = 4,
     "5" = 2
   )
   v.color <- stats::setNames(grDevices::palette()[1:5], 1:5)
   
   # default igraph plotting - no params
   plot(g)
   
   # igraph plotting - custom params
   plot(g, 
        vertex.size = v.size[V(g)$com], 
        vertex.color = v.color[V(g)$com], 
        vertex.label.dist = 1, 
        vertex.label.color = ifelse(V(g)$name %in% input.sample, 
                                    "indianred1", "gray20"), 
        edge.curved = TRUE, 
        edge.width = 3)
   
   
   # you can also remove text by setting labels to ""
   plot(g, 
        vertex.size = v.size[V(g)$com], 
        vertex.color = v.color[V(g)$com], 
        # only show level 1 (pathway) and 5 (compound)
        vertex.label = ifelse(V(g)$com %in% c(1, 5), V(g)$label, ""), 
        vertex.label.dist = 1, 
        vertex.label.color = ifelse(V(g)$name %in% input.sample, 
                                    "indianred1", "gray20"), 
        edge.width = 3)
2. YonghuiDong commented on Mar 6, 2023

   

   YonghuiDong

   on Mar 6, 2023

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   Dear Sergi,

   Thanks a lot for your kind help!

   Dong