How to find the pattern subgraphs in original graph?
1
I have a graph. One can see that the complect subgraph A<->B<->C and E<->D<->F (pattern) occurs twice in the graph. I found the motifs and took 1st and 7th motifs from the list of igraphs.
libraty(igraph)
el <- matrix( c("A", "B",
"A", "C",
"B", "A",
"B", "C",
"C", "A",
"C", "B",
"C", "E",
"E", "D",
"E", "F",
"D", "E",
"D", "F",
"F", "E",
"F", "D"),
nc = 2, byrow = TRUE)
graph <- graph_from_edgelist(el)
pattern <- graph.isocreate(size=3, number = 15, directed=TRUE)
iso <- subgraph_isomorphisms(pattern, graph)
motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) })
V(graph)$id <- seq_len(vcount(graph))
V(graph)$color <- "white"
par(mfrow=c(1,2))
plot(graph, edge.curved=TRUE, main="Original graph")
m1 <- V(motifs[[1]])$id; m2 <- V(motifs[[7]])$id
V(graph)[m1]$color="red"; V(graph)[m2]$color="green"
plot(graph, edge.curved=TRUE, main="Highlight graph")
I have a solution by hand selection motifs[[1]], motifs[[7]].
Question.
How to find the vertex lists of the pattern subgraph (for example, complect subgraph) automatically?
r igraph sna isomorphism
asked Nov 17 '18 at 3:02
NickNick
283112
add a comment |
1
I have a graph. One can see that the complect subgraph A<->B<->C and E<->D<->F (pattern) occurs twice in the graph. I found the motifs and took 1st and 7th motifs from the list of igraphs.
libraty(igraph)
el <- matrix( c("A", "B",
"A", "C",
"B", "A",
"B", "C",
"C", "A",
"C", "B",
"C", "E",
"E", "D",
"E", "F",
"D", "E",
"D", "F",
"F", "E",
"F", "D"),
nc = 2, byrow = TRUE)
graph <- graph_from_edgelist(el)
pattern <- graph.isocreate(size=3, number = 15, directed=TRUE)
iso <- subgraph_isomorphisms(pattern, graph)
motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) })
V(graph)$id <- seq_len(vcount(graph))
V(graph)$color <- "white"
par(mfrow=c(1,2))
plot(graph, edge.curved=TRUE, main="Original graph")
m1 <- V(motifs[[1]])$id; m2 <- V(motifs[[7]])$id
V(graph)[m1]$color="red"; V(graph)[m2]$color="green"
plot(graph, edge.curved=TRUE, main="Highlight graph")
I have a solution by hand selection motifs[[1]], motifs[[7]].
Question.
How to find the vertex lists of the pattern subgraph (for example, complect subgraph) automatically?
r igraph sna isomorphism
asked Nov 17 '18 at 3:02
NickNick
283112
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
1
If you want the equivalent of motifs, usesubgraph_isomorphismswith the LAD method (look up how) andinduced=TRUE.
– Szabolcs
Nov 19 '18 at 12:37
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16
add a comment |
1
1
1
1
I have a graph. One can see that the complect subgraph A<->B<->C and E<->D<->F (pattern) occurs twice in the graph. I found the motifs and took 1st and 7th motifs from the list of igraphs.
libraty(igraph)
el <- matrix( c("A", "B",
"A", "C",
"B", "A",
"B", "C",
"C", "A",
"C", "B",
"C", "E",
"E", "D",
"E", "F",
"D", "E",
"D", "F",
"F", "E",
"F", "D"),
nc = 2, byrow = TRUE)
graph <- graph_from_edgelist(el)
pattern <- graph.isocreate(size=3, number = 15, directed=TRUE)
iso <- subgraph_isomorphisms(pattern, graph)
motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) })
V(graph)$id <- seq_len(vcount(graph))
V(graph)$color <- "white"
par(mfrow=c(1,2))
plot(graph, edge.curved=TRUE, main="Original graph")
m1 <- V(motifs[[1]])$id; m2 <- V(motifs[[7]])$id
V(graph)[m1]$color="red"; V(graph)[m2]$color="green"
plot(graph, edge.curved=TRUE, main="Highlight graph")
I have a solution by hand selection motifs[[1]], motifs[[7]].
Question.
How to find the vertex lists of the pattern subgraph (for example, complect subgraph) automatically?
r igraph sna isomorphism
asked Nov 17 '18 at 3:02
NickNick
283112
I have a graph. One can see that the complect subgraph A<->B<->C and E<->D<->F (pattern) occurs twice in the graph. I found the motifs and took 1st and 7th motifs from the list of igraphs.
libraty(igraph)
el <- matrix( c("A", "B",
"A", "C",
"B", "A",
"B", "C",
"C", "A",
"C", "B",
"C", "E",
"E", "D",
"E", "F",
"D", "E",
"D", "F",
"F", "E",
"F", "D"),
nc = 2, byrow = TRUE)
graph <- graph_from_edgelist(el)
pattern <- graph.isocreate(size=3, number = 15, directed=TRUE)
iso <- subgraph_isomorphisms(pattern, graph)
motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) })
V(graph)$id <- seq_len(vcount(graph))
V(graph)$color <- "white"
par(mfrow=c(1,2))
plot(graph, edge.curved=TRUE, main="Original graph")
m1 <- V(motifs[[1]])$id; m2 <- V(motifs[[7]])$id
V(graph)[m1]$color="red"; V(graph)[m2]$color="green"
plot(graph, edge.curved=TRUE, main="Highlight graph")
I have a solution by hand selection motifs[[1]], motifs[[7]].
Question.
How to find the vertex lists of the pattern subgraph (for example, complect subgraph) automatically?
r igraph sna isomorphism
r igraph sna isomorphism
asked Nov 17 '18 at 3:02
NickNick
283112
asked Nov 17 '18 at 3:02
NickNick
283112
edited Nov 18 '18 at 9:29
Nick
asked Nov 17 '18 at 3:02
NickNick
283112
asked Nov 17 '18 at 3:02
NickNick
283112
asked Nov 17 '18 at 3:02
NickNick
283112
283112
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
1
If you want the equivalent of motifs, usesubgraph_isomorphismswith the LAD method (look up how) andinduced=TRUE.
– Szabolcs
Nov 19 '18 at 12:37
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16
add a comment |
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
1
If you want the equivalent of motifs, usesubgraph_isomorphismswith the LAD method (look up how) andinduced=TRUE.
– Szabolcs
Nov 19 '18 at 12:37
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
1
1
If you want the equivalent of motifs, use
subgraph_isomorphisms with the LAD method (look up how) and induced=TRUE.– Szabolcs
Nov 19 '18 at 12:37
If you want the equivalent of motifs, use
subgraph_isomorphisms with the LAD method (look up how) and induced=TRUE.– Szabolcs
Nov 19 '18 at 12:37
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16
add a comment |
0
active
oldest
votes
Your Answer
StackExchange.ifUsing("editor", function () {
StackExchange.using("externalEditor", function () {
StackExchange.using("snippets", function () {
StackExchange.snippets.init();
});
});
}, "code-snippets");
StackExchange.ready(function() {
var channelOptions = {
tags: "".split(" "),
id: "1"
};
initTagRenderer("".split(" "), "".split(" "), channelOptions);
StackExchange.using("externalEditor", function() {
// Have to fire editor after snippets, if snippets enabled
if (StackExchange.settings.snippets.snippetsEnabled) {
StackExchange.using("snippets", function() {
createEditor();
});
}
else {
createEditor();
}
});
function createEditor() {
StackExchange.prepareEditor({
heartbeatType: 'answer',
autoActivateHeartbeat: false,
convertImagesToLinks: true,
noModals: true,
showLowRepImageUploadWarning: true,
reputationToPostImages: 10,
bindNavPrevention: true,
postfix: "",
imageUploader: {
brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
allowUrls: true
},
onDemand: true,
discardSelector: ".discard-answer"
,immediatelyShowMarkdownHelp:true
});
}
});
draft saved
draft discarded
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53347818%2fhow-to-find-the-pattern-subgraphs-in-original-graph%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
0
active
oldest
votes
0
active
oldest
votes
active
oldest
votes
active
oldest
votes
draft saved
draft discarded
Thanks for contributing an answer to Stack Overflow!
- Please be sure to answer the question. Provide details and share your research!
But avoid …
- Asking for help, clarification, or responding to other answers.
- Making statements based on opinion; back them up with references or personal experience.
To learn more, see our tips on writing great answers.
draft saved
draft discarded
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
StackExchange.ready(
function () {
StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fstackoverflow.com%2fquestions%2f53347818%2fhow-to-find-the-pattern-subgraphs-in-original-graph%23new-answer', 'question_page');
}
);
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Sign up or log in
StackExchange.ready(function () {
StackExchange.helpers.onClickDraftSave('#login-link');
});
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Sign up using Google
Sign up using Facebook
Sign up using Email and Password
Post as a guest
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
Required, but never shown
I removed my solution as I realised something unstable in it. In any case, it is still not entirely clear what you mean by matching or "In graph can be occurred some triads and I need to color them".
– Julius Vainora
Nov 18 '18 at 2:23
1
If you want the equivalent of motifs, use
subgraph_isomorphismswith the LAD method (look up how) andinduced=TRUE.– Szabolcs
Nov 19 '18 at 12:37
@Szabolcs, I have tried change iso <- subgraph_isomorphisms(pattern, graph) motifs <- lapply(iso, function (x) { induced_subgraph(graph, x) }) on the iso <- subgraph_isomorphisms(pattern, graph, methof="lad",induced=TRUE), but I have 12 lists of motifs again. ,
– Nick
Nov 19 '18 at 16:16