r - igraph permute() method bug -

-

i want node permute graph. see test graph have created, below. when use permute() method igraph r library, no changes occur in new graph permute() makes. happening?

testg <- vector(mode="list", length=6); #assign initial probabilities  testg = list("gene1"=0, "gene2"=0, "gene3"=0, "gene4"=0, "gene5"=0, "gene6"=0); adjacency_test <- matrix(c(0,1,1,0,0,0,1,0,1,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0), nrow=6, ncol=6); rownames(adjacency_test) <- c("gene1", "gene2", "gene3","gene4","gene5","gene6"); colnames(adjacency_test) <- c("gene1", "gene2", "gene3","gene4","gene5","gene6"); require(igraph) p <- graph.adjacency(adjacency_test, mode="undirected", weighted=true); vids.permuted <- c(6,5,4,3,2,1) p2 <- permute(p, permutation=vids.permuted) plot(p) plot(p2)

p:

graph p - original graph

p2:

graph p2 - permuted graph of p

i expect clique in permuted graph (p2) gene6, gene5, gene4, not gene1, gene2, , gene3 again, in original.

what happening?

edit:

per response below, correct, had worry. when rearrange node names manually, how come when check if edges same, , degrees same of original graph versus permuted graph, igraph says true? 

p <- graph.adjacency(adjacency_test, mode="undirected", weighted=true); p2 <- p v(p2)$name <- v(p)$name[sample(length(v(p)$name), replace=false)] # p sure different p2 plot(p, layout=layout.reingold.tilford) plot(p2, layout=layout.reingold.tilford) # why degrees still same, , edges still same? all(e(p)==e(p2)) degs1 <- degree(p) degs2 <- degree(p2) all(degs1==degs2)

the permute function swaps vertex ids , creates isomorphic graph. not want. swap vertex labels use,

p2=p v(p2)$name=paste("gene ",6:1)

Comments

Post a Comment

Popular posts from this blog

mysql - Dreamhost PyCharm Django Python 3 Launching a Site -

-
i'm new python/django , created simple django website using pycharm. site works fine running on computer, i'm lost when comes taking site onto host (dreamhost). i'm able upload files correct directories fine, , believe made correct changes database on mysql. i'm not sure go there though. right now, page shows files rather site. direction appreciated. much! you should not run django application using python manage.py runserver on production. how run application on django depends on server (apache, nginx) want use for apache - https://docs.djangoproject.com/en/1.10/howto/deployment/wsgi/modwsgi/ for nginx - https://www.digitalocean.com/community/tutorials/how-to-serve-django-applications-with-uwsgi-and-nginx-on-ubuntu-14-04 the mysql database should, of course, exist , have correct credentials. or, if choose use sqlite, file should accessible, readable , writable www-user (may different depending on linux distributive)
Read more

java - Sending SMS with SMSLib and Web Services -

-
i have made rest web service send smss using hsdpa usb modem. using smslib in java send smss. every time web service invoked, create gateway start service, send message, stop service , remove gateway. takes 20 seconds each message. found starting service takes lot of time. part of code use send smss service.getinstance().addgateway(gateway); service.getinstance().startservice(); outboundmessage msg = new outboundmessage(phonenumber, message); if (service.getinstance().sendmessage(msg)) { result = "message sent successfully!!"; } else { result = "could not send message."; } service.getinstance().stopservice(); service.getinstance().removegateway(gateway);//remove gateway is there way can start service once if not started , use send message when ever web service invoked? why dont group messages , send in 1 go? service.getinstance().sendmessages(messa...
Read more

java - How to resolve The method toString() in the type Object is not applicable for the arguments (InputStream) -

-
i'm trying read json file local machine. @path("/") public class jsonparsing { file f = new file("file.json"); if (f.exists()){ inputstream = new fileinputstream("file.json"); string jsontxt = ioutils.tostring(is); system.out.println(jsontxt); jsonobject json = new jsonobject(jsontxt); string = json.getstring("1000"); system.out.println(a); } } but i'm getting error in tostring() method. possible read .txt file containing json object local machine? if possible, how done? firstly: whenever ask question- add imports well. secondly: yes possible read .txt file containing json object. steps: 1. add maven dependency in pom.xml - <dependency> <groupid>com.googlecode.json-simple</groupid> <artifactid>json-simple</artifactid> <version>1.1.1</version> </dependency> or add jar of dependency. 2.import...
Read more