I have plotted a network graph using d3 library but as the number of nodes grow, animation takes a huge performance toll. For analytics, I do not need good UI but something quick
Question: How do I stop the real-time simulation and yet still enable manipulation of the graph?
Working Code Example
require(igraph)
require(networkD3)
# Use igraph to make the graph and find membership
karate <- make_graph("Zachary")
wc <- cluster_walktrap(karate)
members <- membership(wc)
# Convert to object suitable for networkD3
karate_d3 <- igraph_to_networkD3(karate, group = members)
# Create force directed network plot
forceNetwork(Links = karate_d3$links, Nodes = karate_d3$nodes,
Source = 'source', Target = 'target', NodeID = 'name',
Group = 'group')
Visual Output:
Related
I'm in the process of creating a weighted igraph network object from a edge list containing two columns from and to. It has proven to be somewhat challenging for me, because when doing a workaround, I notice changes in the network metrics and I believe I'm doing something wrong.
library(igraph)
links <- read.csv2("edgelist.csv")
vertices <- read.csv2("vertices.csv")
network <- graph_from_data_frame(d=links,vertices = vertices,directed = TRUE)
##the following step is included to remove self-loops that I have used to include all isolate nodes to the network##
network <- simplify(network,remove.multiple = FALSE, remove.loops = TRUE)
In this situation I have successfully created a network object. However, it is not weighted. Therefore I create a second network object by taking the adjacency matrix from the objected created earlier and creating the new igraph object from it like this:
gettheweights <- get.adjacency(network)
network2 <- graph_from_adjacency_matrix(gettheweights,mode = "directed",weighted = TRUE)
However, after this when I call both of the objects, I notice a difference in the number of edges, why is this?
network2
IGRAPH ef31b3a DNW- 200 1092 --
network
IGRAPH 934d444 DN-- 200 3626 --
Additionally, I believe I've done something wrong because if they indeed would be the same network, shouldn't their densities be the same? Now it is not the case:
graph.density(network2)
[1] 0.02743719
graph.density(network)
[1] 0.09110553
I browsed and tried several different answers found from here but many were not 1:1 identical and I failed to find a solution.
All seems to be in order. When you re-project a network with edge-duplicates to be represented as a weight by the number of edges between given vertices, the density of your graph should change.
When you you test graph.density(network2) and graph.density(network), they should be different if indeed edge-duplicates were reduced to single-edges with weight as an edge attribute, as your output from network2 and network suggest.
This (over-) commented code goes through the process.
library(igraph)
# Data that should resemble yours
edges <- data.frame(from=c("A","B","C","D","E","A","A","A","B","C"),
to =c("A","C","D","A","B","B","B","C","B","D"))
vertices <- unique(unlist(edges))
# Building graphh in the same way as you do
g0 <- graph_from_data_frame(d=edges, vertices=vertices, directed = TRUE)
# Note that the graph is "DN--": directed, named, but NOT Weighted, since
# Instead of weighted edges, we have a whole lot of dubble edges
(g0)
plot(g0)
# We can se the dubble edges in the adjacency matrix as >1
get.adjacency(g0)
# Use simplify to remove LOOPS ONLY as we can see in the adjacency metrix test
g1 <- simplify(g0, remove.multiple = FALSE, remove.loops = TRUE)
get.adjacency(g1) == get.adjacency(g0)
# Turn the multiple edges into edge-weights by jumping through an adjacency matrix
g2 <- graph_from_adjacency_matrix(get.adjacency(g1), mode = "directed", weighted = TRUE)
# Instead of multiple edges (like many links between "A" and "B"), there are now
# just single edges with weights (hence the density of the network's changed).
graph.density(g1) == graph.density(g2)
# The former doubble edges are now here:
E(g2)$weight
# And we can see that the g2 is now "Named-Directed-Weighted" where g1 was only
# "Named-Directed" and no weights.
(g1);(g2)
# Let's plot the weights
E(g2)$width = E(g2)$weight*5
plot(g2)
A shortcoming of this/your method, however, is that the adjacency matrix is able to carry only the edge-count between any given vertices. If your edge-list contains more variables than i and j, the use of graph_from_data_frame() would normally embed edge-attributes of those variables for you straight from your csv-import (which is nice).
When you convert the edges into weights, however, you would loose that information. And, come to think of it, that information would have to be "converted" too. What would we do with two edges between the same vertices that have different edge-attributes?
At this point, the answer goes slightly beyond your question, but still stays in the realm of explaining the relation between graphs of multiple edges between the same vertices and their representation as weighted graphs with only one structural edge per verticy.
To convert edge-attributes along this transformation into a weighted graph, I suggest you'd use dplyr to "rebuild" any edge-attributes manually in order to keep control of how they are supposed to be merged down when recasting into a weighted one.
This picks up where the code above left off:
# Let's imagine that our original network had these two edge-attributes
E(g0)$coolness <- c(1,2,1,2,3,2,3,3,2,2)
E(g0)$hotness <- c(9,8,2,3,4,5,6,7,8,9)
# Plot the hotness
E(g0)$color <- colorRampPalette(c("green", "red"))(10)[E(g0)$hotness]
plot(g0)
# Note that the hotness between C and D are very different
# When we make your transformations for a weighted netowk, we loose the coolness
# and hotness information
g2 <- g0 %>% simplify(remove.multiple = FALSE, remove.loops = TRUE) %>%
get.adjacency() %>%
graph_from_adjacency_matrix(mode = "directed", weighted = TRUE)
g2$hotness # Naturally, the edge-attributes were lost!
# We can use dplyr to take controll over how we'd like the edge-attributes transfered
# when multiple edges in g0 with different edge attributes are supposed to merge into
# one single edge
library(dplyr)
recalculated_edge_attributes <-
data.frame(name = ends(g0, E(g0)) %>% as.data.frame() %>% unite("name", V1:V2, sep="->"),
hotness = E(g0)$hotness) %>%
group_by(name) %>%
summarise(mean_hotness = mean(hotness))
# We used a string-version of the names of connected verticies (like "A->B") to refere
# to the attributes of each edge. This can now be used to merge back the re-calculated
# edge-attributes onto the weighted graph in g2
g2_attributes <- data.frame(name = ends(g2, E(g2)) %>% as.data.frame() %>% unite("name", V1:V2, sep="->")) %>%
left_join(recalculated_edge_attributes, by="name")
# And manually re-attatch our mean-attributes onto the g2 network
E(g2)$mean_hotness <- g2_attributes$mean_hotness
E(g2)$color <- colorRampPalette(c("green", "red"))(max(E(g2)$mean_hotness))[E(g2)$mean_hotness]
# Note how the link between A and B has turned into the brown mean of the two previous
# green and red hotness-edges
plot(g2)
Sometimes, your analyses may benefit from either structure (weighted no duplicates or unweighted with duplicates). Algorithms for, for example, shortest paths are able to incorporate edge-weight as described in this answer, but other analyses might not allow for or be intuitive when using the weighted version of your network data.
Let purpose guide your structure.
I am calculating louvain communities on graphs of communications data, where vertices represent performers on a big project. The graphs represent different communication methods (e.g., email, phone).
We want to try to identify teams of performers from their communication data. Since performers have preferences for different communication methods, the graphs are of different sizes and may have some unique vertices which may not be present in both. When I try to compare the community objects from the respective graphs, igraph::compare() throws an exception. See toy reprex below.
I considered a dplyr::full_join() or inner_join() of the vertex lists before constructing the graph & community objects to make them the same size, but worry about the impact of doing so on the resulting cluster_louvain() solutions.
Any ideas on how I can compare the community objects to one another from these different communication methods? Thanks in advance!
library(tidyverse, warn.conflicts = FALSE)
library(igraph, warn.conflicts = FALSE)
nodes <- as_tibble(list(id = c("sample1", "sample2", "sample3")))
edge <- as_tibble(list(from = "sample1",
to = "sample2"))
net <- graph_from_data_frame(d = edge, vertices = nodes, directed = FALSE)
com <- cluster_louvain(net)
nodes2 <- as_tibble(list(id = c("sample1","sample21", "sample22","sample23"
)))
edge2 <- as_tibble(list(from = c("sample1", "sample21"),
to = c("sample21", "sample22")))
net2 <- graph_from_data_frame(d = edge2, vertices = nodes2, directed = FALSE)
com2 <- cluster_louvain(net2)
# # uncomment to see graph plots
# plot.igraph(net, mark.groups = com)
# plot.igraph(net2, mark.groups = com2)
compare(com, com2)
#> Error in i_compare(comm1, comm2, method): At community.c:3106 : community membership vectors have different lengths, Invalid value
Created on 2019-02-22 by the reprex package (v0.2.1)
You will not (I don't believe) be able to compare clustering algorithms from two different graphs that contain two different sets of nodes. Practically you can't do it in igraph and conceptually its hard because the way clustering algorithms are compared is by considering all pairs of nodes in a graph and checking whether they are placed in the same cluster or a different cluster in each of the two clustering approaches. If both clustering approaches typically put the same nodes together and the same nodes apart then they are considered more similar.1
I suppose another valid way to approach the problem would be to evaluate how similar the clustering schemes are for purely the set of nodes that are the intersection of the two graphs. You'll have to decide what makes more sense in your setting. I'll show how to do it using the union of nodes rather than the intersection.
So you need all the same nodes in both graphs in order to make the comparison. In fact, I think the easier way to do it is to put all the same nodes in one graph and have different edge types. Then you can compute your clusters for each edge type separately and then make the comparison. The reprex below is hopefully clear:
# repeat your set-up
library(tidyverse, warn.conflicts = FALSE)
library(igraph, warn.conflicts = FALSE)
nodes <- as_tibble(list(id = c("sample1", "sample2", "sample3")))
edge <- as_tibble(list(from = "sample1",
to = "sample2"))
nodes2 <- as_tibble(list(id = c("sample1","sample21", "sample22","sample23")))
edge2 <- as_tibble(list(from = c("sample1", "sample21"),
to = c("sample21", "sample22")))
# approach from a single graph
# concatenate edges
edges <- rbind(edge, edge2)
# create an edge attribute indicating network type
edges$type <- c("phone", "email", "email")
# the set of nodes (across both graphs)
nodes <- unique(rbind(nodes, nodes2))
g <- graph_from_data_frame(d = edges, vertices = nodes, directed = F)
# We cluster over the graph without the email edges
com_phone <- cluster_louvain(g %>% delete_edges(E(g)[E(g)$type=="email"]))
plot(g, mark.groups = com_phone)
# Now we can cluster over the graph without the phone edges
com_email <- cluster_louvain(g %>% delete_edges(E(g)[E(g)$type=="phone"]))
plot(g, mark.groups = com_email)
# Now we can compare
compare(com_phone, com_email)
#> [1] 0.7803552
As you can see from the plots we pick out the same initial clustering structure you found in the separate graphs with the additions of the extra isolated nodes.
1: Obviously this is a pretty vague explanation. The default algorithm used in compare is from this paper, which has a nice discussion.
I'm trying to use data.tree and NetworkD3 in R to create a tree representation of a file system where the nodes of the graph are weighted by file size.
library(data.tree)
library(networkD3)
repo <- Node$new("Repository")
git <- repo$AddChild(".git")
prod <- repo$AddChild("Production")
exp <- repo$AddChild("Experimental")
repo$size <- 866000
git$size <- 661000
prod$size <- 153000
exp$size <- 48000
I can get a vector of these sizes using Get, so that
sizes <- repo$Get("size")
But when I try to put it all together, I'm not sure how to include this weight information in the network visualization step. Trying to do something like this...
reponet <- ToDataFrameNetwork(repo,"repo")
net <- forceNetwork(reponet, Nodesize = repo$Get("size"))
to no avail. Basically I'm trying to do what Julia Silge did in this great SO blog post. Does anyone know how to set this?
Check the help file for forceNetwork... there are numerous, mandatory parameters that you have not set.
You can use simpleNetwork to plot a network with just a links data frame like you have, but it doesn't allow you to control the node size... for example...
simpleNetwork(reponet)
To control the node size, you need to use forceNetwork, but it requires a links data frame and a nodes data frame. You could build the nodes data frame from the sizes object you created, and then adjust the source and target IDs in your links data frame to match the indexes of the appropriate node in your nodes data frame (0 indexed because it's sent to JavaScript)... for example...
nodesdf <- data.frame(name = names(sizes), nodesize = sizes / 10000, group = 1)
reponet$from <- match(reponet$from, nodesdf$name) - 1
reponet$to <- match(reponet$to, nodesdf$name) - 1
forceNetwork(reponet, Nodes = nodesdf, Source = "from", Target = "to",
NodeID = "name", Group = "group", Nodesize = "nodesize")
I have a xlsx contains about 2000+ nodes and 9000 edges. And I want to generate a explicit directed graph. I tried igraph package in R to generate the directed graph I want but (1) it is too many nodes and edges to print clearly.I refer some documents that using networkd3 to convert igraph to networkd3 and plot,but(2) the direction(arrows) lost.
Would you please help me out these sitution? Either (1) or (2).My codes belows,and my data format like
edges1.xlsx
source target attr
s1 s2 a
s2 s7 b
s2 s3 c
nodes1.xlsx
id attr
s1 a
s2 c
s3 d
s4 c
library(readxl)
library(igraph)
links <- read_excel("C:\\Users\\file\\Desktop\\1W\\edges1.xlsx",sheet=1,col_names = TRUE)
nodes <- read_excel("C:\\Users\\file\\Desktop\\1W\\nodes1.xlsx",sheet=1,col_names = TRUE)
net <- graph_from_data_frame(d=links,vertices=unique(nodes$JYZH),directed = T)
plot(net, vertex.color="orange",vertex.size=.1,vertex.label=NA,vertex.label.color="black",vertex.label.dist=0,edge.arrow.size=.01)
#above work well with my data format but because it is too many nodes(2000+) and edges(9000+) to print clearly
library(networkD3)
#Use igraph to make the graph and find membership
wc <- cluster_walktrap(net)
members <- membership(wc)
#Convert to object suitable for networkD3
net_d3 <- igraph_to_networkD3(net,group = members)
forceNetwork(Links = net_d3$links, Nodes = net_d3$nodes,
Source = 'source', Target = 'target', NodeID = 'name',Group = 'group', zoom = TRUE)
#using above code of networkd3,the direction lost.....
Is there any solutions to solve these problems?
A network graph with 2000+ nodes and 9000 edges is going to be messy no matter which software you use to generate it. What do you hope will be different if you plot it with networkD3?
UPDATE (2017.03.24): This feature (using arrowheads to show the direction of edges/links) is in the most recent released version (0.4) of networkD3 with the arrows = TRUE argument to forceNetwork().
I am using R to visualize relation between, say, 5-6 different nodes. Now, a graph is probably the best way to do it. The issue is, the edges are way too many. There can be a hundred edges between two vertexes. That makes the graph look very clumsy. I want the edge name to be displayed. With a hundred edge name being displayed, they overlap over each other and hence not comprehensible.
So, I have two questions-
Is there any other way in which I can represent the data? Some kind of chart probably?
I want to export the final output to HTML, which uses d3.js or any other similar library, keeping the edge name and a few other similar information intact. What will be the best plugin to use in that case?
I am using the igraph library to create the graph in R.
I also tried using the networkD3 library to export it to an HTML and make it interactive.
graph <- graph.data.frame(edges, directed = TRUE, vertices = vertex)
plot(graph, edge.label = E(graph)$name)
wc <- cluster_walktrap(graph)
members <- membership(wc)
graph_d3 <- igraph_to_networkD3(graph, group = members)
graph_forceNetwork <- forceNetwork(Links = graph_d3$links, Nodes = graph_d3$nodes,
Source = 'source',
Target = 'target',
NodeID = 'name',
Group = 'group',
zoom = TRUE,
fontSize = 20)
Right now, it is a graph with only two vertex and about 60-70 edges between them. So, I did not use any particular layout.