CODEWITHSUNDEEP
rplotigraph
Jonno Bourne
Jonno Bourne

Reputation: 1991

Plot two igraph networks using the same coordinates and same placement in the plot frame

I am trying to plot a network that changes in time. The network starts with a certain number of nodes and edges and each time step some of the nodes and edges are removed.

I want to be able to plot the network so that the nodes are in the same place in each. However when I try this. sometimes the nodes shift position in the plot frame even if the relation to each other is the same.

I am making the network change into a gif so even small changes are annoying. I think the change may occur when a large fraction of the nodes are removed but I am not sure.

The code below illustrates this using an ER graph.

library(igraph); library(dplyr)

#generate random graph
set.seed(500)
RandomGraph <- sample_gnm(1000, 2500)

#name nodes
V(RandomGraph)$name <- paste0("Node", 1:1000)

#Get the coordinates of the Nodes
Coords <- layout_with_fr(RandomGraph) %>% 
  as_tibble %>%
    bind_cols(data_frame(names = names(V(RandomGraph))))

#Delete random vertices
deletevertex <-sample( V(RandomGraph)$name, 400)

RandomGraph2 <-delete.vertices(RandomGraph, deletevertex)

#get the coordinates of the remaining Nodes
  NetCoords <- data_frame(names = names(V(RandomGraph2))) %>%
    left_join(Coords, by= "names")

#plot both graphs

RandomGraph%>% 
  plot(.,vertex.size=.8, edge.arrow.size=.4, vertex.label = NA, layout = as.matrix(Coords[,1:2]))

RandomGraph2%>% 
  plot(.,vertex.size=.8, edge.arrow.size=.4, vertex.label = NA, layout = as.matrix(NetCoords[,2:3]))

#They nodes have the same relationship to each other but are not laid out in the same position in the frame

As you can see the plots have placed nodes in the same place relative to each other but not relative to the frame.

How can I have the plot position fixed.

Upvotes: 2

Views: 1982

Answers (2)

lukeA
lukeA

Reputation: 54257

The problem is that 

identical(range(Coords[1]), range(NetCoords[2]))
# [1] FALSE

Since igraph normalizes the coordinates on a range between -1 and 1 before plotting, this leads to slightly different coordinates for NetCoords compared to Coords. I'd just calculate the normalized coordinates for all nodes beforehand:

coords_rescaled <- sapply(Coords[-3], function(x) -1+((x-min(x))*2)/diff(range(x)))
rownames(coords_rescaled) <- Coords$names

And then assign the normalized coordinates (or the required subset) and set rescale=FALSE (as @jul) already suggested: 

par(mfrow=c(1,2), mar=c(1,.5,1,.5))
RandomGraph%>% 
  plot(.,edge.arrow.size=.4, layout = coords_rescaled, rescale=F);box()
RandomGraph2%>% 
  plot(.,edge.arrow.size=.4, layout = coords_rescaled[NetCoords$names, ], rescale=F);box()

Upvotes: 2

Jul
Jul

Reputation: 1139

plot.igraph rescales each axis by default (from -1 to +1 on both x and y).

You just need to turn that off: rescale = F and then explicitly set appropriate xlim and ylim values.

For your example code..

RandomGraph%>% 
  plot(.,vertex.size=.8, edge.arrow.size=.4, vertex.label = NA, layout = as.matrix(Coords[,1:2]),rescale=F,xlim=c(-25,30),ylim=c(-20,35))

RandomGraph2%>% 
  plot(.,vertex.size=.8, edge.arrow.size=.4, vertex.label = NA, layout = as.matrix(NetCoords[,2:3]),rescale=F,xlim=c(-25,30),ylim=c(-20,35))

Upvotes: 2

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