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

[YonghuiDong]

Dear developer,

Thanks for this amazing R package.

I want to display only the metabolite and pathway names as show in your original publication, how can I achieve that?

I did not find the corresponding parameter in plotGraph function.

Thanks a lot.

Dong

** Fig. 1** Figure from the original publication where only metabolite and pathway names were displayed.

Fig. 2 Figure produced using plotGraph function in which all names were shown in the plot.

[SergiPicart]

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)

[YonghuiDong]

Dear Sergi,

Thanks a lot for your kind help!

Dong