How to get on ggraph the same plot as with RCy3 (Cytoscape)

Question

I can get thanks to the function RCy3::getNodePosition() x and y coordinates from a graph plot drawn with RCy3 on Cytoscape. Then, I can use ggraph with layout based on the dataframe prepared from coordinates. I have got a graph but with a deeply different structure from the previous one. What could explain this difference?

Consider the following example coming from: http://cytoscape.org/RCy3/articles/Network-functions-and-visualization.html

'''

library(RCy3)
library(ggraph)

'''

lesmis <- system.file("extdata","lesmis.txt", package="RCy3")
dataSet <- read.table(lesmis, header = FALSE, sep = "	")

'''

Create a graph. Use simplify to ensure that there are no duplicated edges or self loops

'''

gD <- igraph::simplify(igraph::graph.data.frame(dataSet, directed=FALSE))

'''

Verify the number of nodes (77) and edges (254):

'''

igraph::vcount(gD)
igraph::ecount(gD)

'''

create the graph gD on Cytoscape '''

createNetworkFromIgraph(gD,new.title='Les Miserables')

'''

create a graph using ggraph

'''

ggraph(gD, layout = 'kk') + 
  geom_edge_link(color = "orange", width=0.7) +
  geom_node_point(size=5, color="gray50")+
  geom_node_text(aes(label = vlabels_1), size=2, color="gray50", repel=T) +
  theme_void()

'''

It is qualitatively the same graph obtained by ggraph as on Cytoscape by using RCy3::createNetworkFromIgraph()

Then, we can get coordinates from graph on Cytoscape as following:

'''

mygraph_Miserables <- createIgraphFromNetwork()
mylayout_Miserables <- getNodePosition()

mylayout_Miserables$x_location <- as.numeric(as.character(mylayout_Miserables$x_location))

mylayout_Miserables$y_location <- as.numeric(as.character(mylayout_Miserables$y_location))

colnames(mylayout_Miserables) <- c('x','y')

vlabels_1 <- get.vertex.attribute(gD, "name")
color_labels_1 <- getNodeColor(vlabels_1)

ggraph(mygraph_Miserables, layout = mylayout_Miserables) + 
  geom_edge_link(color = "orange", width=0.7) +
  geom_node_point(size=5, color="gray50") +
  geom_node_text(aes(label = vlabels_1), size=2, color="gray50", repel=T) +
  theme_void()

'''

This new graph obtained by ggraph using layout = mylayout_Miserables doesn't provide the same structure of the graph provide directly by ggraph or by RCy3. How can we explain that?

Alain Paris

How to get on ggraph the same plot as with RCy3 (Cytoscape)

0 Answers