Creating new graph basing on cluster anylise - R
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library("network")
library("networkD3")
library("igraph")
df1 <- read.table(text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5", header = TRUE)
lesmis <- graph_from_data_frame(df1)
wc <- cluster_walktrap(lesmis)
members <- membership(wc)
lesmis <- igraph_to_networkD3(lesmis, group = members)
D3_network_LM <- networkD3::forceNetwork(Links = lesmis$links, Nodes = lesmis$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'group',
opacity = 1,zoom = TRUE)
networkD3::saveNetwork(D3_network_LM, "test.html", selfcontained = TRUE)
So close we got a network. After that we create new graph by merging several vertices into one. In our case those vertices that belong to particular community.
lesmis <- graph_from_data_frame(df1)
cg <- contract.vertices(lesmis, members)
ay <- as_long_data_frame(cg)
View(ay)
we got new graph,
from to
1 2
We may built again new graph where now these nodes are the groups, but their names are 1 and 2, my question is how we can add clients names to this new graph. So that, when hovering , we may get not only the number of the node(group) but also the list of client that belongs to this new node(group).
r igraph htmlwidgets networkd3
asked Nov 20 at 13:44
Maksym Moroz
249
add a comment |
up vote
0
down vote
favorite
library("network")
library("networkD3")
library("igraph")
df1 <- read.table(text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5", header = TRUE)
lesmis <- graph_from_data_frame(df1)
wc <- cluster_walktrap(lesmis)
members <- membership(wc)
lesmis <- igraph_to_networkD3(lesmis, group = members)
D3_network_LM <- networkD3::forceNetwork(Links = lesmis$links, Nodes = lesmis$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'group',
opacity = 1,zoom = TRUE)
networkD3::saveNetwork(D3_network_LM, "test.html", selfcontained = TRUE)
So close we got a network. After that we create new graph by merging several vertices into one. In our case those vertices that belong to particular community.
lesmis <- graph_from_data_frame(df1)
cg <- contract.vertices(lesmis, members)
ay <- as_long_data_frame(cg)
View(ay)
we got new graph,
from to
1 2
We may built again new graph where now these nodes are the groups, but their names are 1 and 2, my question is how we can add clients names to this new graph. So that, when hovering , we may get not only the number of the node(group) but also the list of client that belongs to this new node(group).
r igraph htmlwidgets networkd3
asked Nov 20 at 13:44
Maksym Moroz
249
I think heregraph_from_data_frame(bank)you meangraph_from_data_frame(df1)to make the example work, and the second part imho is not working, havingError in contract.vertices(lesmis, members) : Not a graph object.
– s_t
Nov 20 at 15:14
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
library("network")
library("networkD3")
library("igraph")
df1 <- read.table(text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5", header = TRUE)
lesmis <- graph_from_data_frame(df1)
wc <- cluster_walktrap(lesmis)
members <- membership(wc)
lesmis <- igraph_to_networkD3(lesmis, group = members)
D3_network_LM <- networkD3::forceNetwork(Links = lesmis$links, Nodes = lesmis$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'group',
opacity = 1,zoom = TRUE)
networkD3::saveNetwork(D3_network_LM, "test.html", selfcontained = TRUE)
So close we got a network. After that we create new graph by merging several vertices into one. In our case those vertices that belong to particular community.
lesmis <- graph_from_data_frame(df1)
cg <- contract.vertices(lesmis, members)
ay <- as_long_data_frame(cg)
View(ay)
we got new graph,
from to
1 2
We may built again new graph where now these nodes are the groups, but their names are 1 and 2, my question is how we can add clients names to this new graph. So that, when hovering , we may get not only the number of the node(group) but also the list of client that belongs to this new node(group).
r igraph htmlwidgets networkd3
asked Nov 20 at 13:44
Maksym Moroz
249
library("network")
library("networkD3")
library("igraph")
df1 <- read.table(text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5", header = TRUE)
lesmis <- graph_from_data_frame(df1)
wc <- cluster_walktrap(lesmis)
members <- membership(wc)
lesmis <- igraph_to_networkD3(lesmis, group = members)
D3_network_LM <- networkD3::forceNetwork(Links = lesmis$links, Nodes = lesmis$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'group',
opacity = 1,zoom = TRUE)
networkD3::saveNetwork(D3_network_LM, "test.html", selfcontained = TRUE)
So close we got a network. After that we create new graph by merging several vertices into one. In our case those vertices that belong to particular community.
lesmis <- graph_from_data_frame(df1)
cg <- contract.vertices(lesmis, members)
ay <- as_long_data_frame(cg)
View(ay)
we got new graph,
from to
1 2
We may built again new graph where now these nodes are the groups, but their names are 1 and 2, my question is how we can add clients names to this new graph. So that, when hovering , we may get not only the number of the node(group) but also the list of client that belongs to this new node(group).
r igraph htmlwidgets networkd3
r igraph htmlwidgets networkd3
asked Nov 20 at 13:44
Maksym Moroz
249
asked Nov 20 at 13:44
Maksym Moroz
249
edited Nov 21 at 7:14
asked Nov 20 at 13:44
Maksym Moroz
249
asked Nov 20 at 13:44
Maksym Moroz
249
asked Nov 20 at 13:44
Maksym Moroz
249
249
I think heregraph_from_data_frame(bank)you meangraph_from_data_frame(df1)to make the example work, and the second part imho is not working, havingError in contract.vertices(lesmis, members) : Not a graph object.
– s_t
Nov 20 at 15:14
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20
add a comment |
I think heregraph_from_data_frame(bank)you meangraph_from_data_frame(df1)to make the example work, and the second part imho is not working, havingError in contract.vertices(lesmis, members) : Not a graph object.
– s_t
Nov 20 at 15:14
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20
I think here
graph_from_data_frame(bank) you mean graph_from_data_frame(df1) to make the example work, and the second part imho is not working, having Error in contract.vertices(lesmis, members) : Not a graph object.– s_t
Nov 20 at 15:14
I think here
graph_from_data_frame(bank) you mean graph_from_data_frame(df1) to make the example work, and the second part imho is not working, having Error in contract.vertices(lesmis, members) : Not a graph object.– s_t
Nov 20 at 15:14
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20
add a comment |
1 Answer
1
active
oldest
votes
up vote
0
down vote
accepted
Your example code doesn't work for multiple reasons (I edited it a bit to fix some obvious problems), but I think the following achieves what you're trying to do...
library(network)
library(networkD3)
library(igraph)
df <- read.table(header = TRUE,
text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5")
df_graph <- graph_from_data_frame(df)
wc <- cluster_walktrap(df_graph)
members <- membership(wc)
df_graph_cntrctd <- contract(df_graph, members, vertex.attr.comb = toString)
df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd)
networkD3::forceNetwork(Links = df_graph_cntrctd_D3$links,
Nodes = df_graph_cntrctd_D3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'name',
opacity = 1, zoom = TRUE)
answered Nov 21 at 1:00
CJ Yetman
3,7352529
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
|
show 2 more comments
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
Your example code doesn't work for multiple reasons (I edited it a bit to fix some obvious problems), but I think the following achieves what you're trying to do...
library(network)
library(networkD3)
library(igraph)
df <- read.table(header = TRUE,
text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5")
df_graph <- graph_from_data_frame(df)
wc <- cluster_walktrap(df_graph)
members <- membership(wc)
df_graph_cntrctd <- contract(df_graph, members, vertex.attr.comb = toString)
df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd)
networkD3::forceNetwork(Links = df_graph_cntrctd_D3$links,
Nodes = df_graph_cntrctd_D3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'name',
opacity = 1, zoom = TRUE)
answered Nov 21 at 1:00
CJ Yetman
3,7352529
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
|
show 2 more comments
up vote
0
down vote
accepted
Your example code doesn't work for multiple reasons (I edited it a bit to fix some obvious problems), but I think the following achieves what you're trying to do...
library(network)
library(networkD3)
library(igraph)
df <- read.table(header = TRUE,
text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5")
df_graph <- graph_from_data_frame(df)
wc <- cluster_walktrap(df_graph)
members <- membership(wc)
df_graph_cntrctd <- contract(df_graph, members, vertex.attr.comb = toString)
df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd)
networkD3::forceNetwork(Links = df_graph_cntrctd_D3$links,
Nodes = df_graph_cntrctd_D3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'name',
opacity = 1, zoom = TRUE)
answered Nov 21 at 1:00
CJ Yetman
3,7352529
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
|
show 2 more comments
up vote
0
down vote
accepted
up vote
0
down vote
accepted
Your example code doesn't work for multiple reasons (I edited it a bit to fix some obvious problems), but I think the following achieves what you're trying to do...
library(network)
library(networkD3)
library(igraph)
df <- read.table(header = TRUE,
text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5")
df_graph <- graph_from_data_frame(df)
wc <- cluster_walktrap(df_graph)
members <- membership(wc)
df_graph_cntrctd <- contract(df_graph, members, vertex.attr.comb = toString)
df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd)
networkD3::forceNetwork(Links = df_graph_cntrctd_D3$links,
Nodes = df_graph_cntrctd_D3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'name',
opacity = 1, zoom = TRUE)
answered Nov 21 at 1:00
CJ Yetman
3,7352529
Your example code doesn't work for multiple reasons (I edited it a bit to fix some obvious problems), but I think the following achieves what you're trying to do...
library(network)
library(networkD3)
library(igraph)
df <- read.table(header = TRUE,
text = "src target
cllient1 cllient2
cllient1 cllient4
cllient1 cllient6
cllient2 cllient3
cllient4 cllient1
cllient4 cllient3
cllient5 cllient6
cllient6 cllient5")
df_graph <- graph_from_data_frame(df)
wc <- cluster_walktrap(df_graph)
members <- membership(wc)
df_graph_cntrctd <- contract(df_graph, members, vertex.attr.comb = toString)
df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd)
networkD3::forceNetwork(Links = df_graph_cntrctd_D3$links,
Nodes = df_graph_cntrctd_D3$nodes,
Source = 'source', Target = 'target',
NodeID = 'name', Group = 'name',
opacity = 1, zoom = TRUE)
answered Nov 21 at 1:00
CJ Yetman
3,7352529
answered Nov 21 at 1:00
CJ Yetman
3,7352529
answered Nov 21 at 1:00
CJ Yetman
3,7352529
answered Nov 21 at 1:00
CJ Yetman
3,7352529
3,7352529
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
|
show 2 more comments
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
yep, sorry for that silly mistakes.. Your suggestion solves what I was asking about :) Thanks a lot.
– Maksym Moroz
Nov 21 at 7:18
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
Can you edit your original question with a reproducible example and/or the exact error message?
– CJ Yetman
Nov 21 at 9:49
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
But as my real graph is more bigger, unfortunately I got an error after this line of code df_graph_cntrctd_D3 <- igraph_to_networkD3(df_graph_cntrctd) Cannot allocate vector on some point because of lack of ram memory I suppose. Is there possible way to use my hdd memory to solve this problem?
– Maksym Moroz
Nov 21 at 9:53
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
Error: cannot allocate vector of size 40 Kb
– Maksym Moroz
Nov 21 at 10:00
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
So I have more clients names and the length of name of each client in every group is bigger than in our example, therefore my RAM ends up quickly
– Maksym Moroz
Nov 21 at 10:48
|
show 2 more comments
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I think here
graph_from_data_frame(bank)you meangraph_from_data_frame(df1)to make the example work, and the second part imho is not working, havingError in contract.vertices(lesmis, members) : Not a graph object.– s_t
Nov 20 at 15:14
Have edited, thank you
– Maksym Moroz
Nov 21 at 7:20