Re: [igraph] randomize network with more controls
You remove the original edges and then add the new ones ;) Or, even better, convert the graph to an adjacency list, do the rewiring there, and then convert the adjacency list back to a graph. T. T. On Thu, Sep 3, 2015 at 9:41 PM, Qunawei Zhang wrote: > Thanks. Is there a function, by which I can rewire two selected edges? > > Best > Quanwei > > On 9/3/15 3:38 PM, "Tamas Nepusz" wrote: > >>Hi, >> >>There is no built-in function for this in igraph; you'll have to >>implement the rewiring process yourself. >> >>T. >>T. >> >> >>On Thu, Sep 3, 2015 at 6:25 PM, Qunawei Zhang >>wrote: >>> Hello: >>> >>> I know how to use rewire and deSeq to randomize a network and keep the >>> degree of the nodes. >>> I have a protein-protein interaction network (192 nodes and 561 edges). >>> Unlike other protein-protein interaction network, I found the >>>interactions >>> among hubs are not suppressed. I want to test whether this topology will >>> make the subnetwork more vulnerable for random attacks. >>> So I need some random network for comparison. To randomize the network >>>I >>> want to reduce the interactions among hub genes and on the other hand >>> increase the number of interactions among hubs and non hubs. Is it >>>possible >>> to used some existing method in igraph to get this? >>> >>> Many thanks >>> >>> Best >>> Quanwei >>> >>> >>> >>> ___ >>> igraph-help mailing list >>> igraph-help@nongnu.org >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >> >>___ >>igraph-help mailing list >>igraph-help@nongnu.org >>https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > ___ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
Re: [igraph] randomize network with more controls
Thanks. Is there a function, by which I can rewire two selected edges? Best Quanwei On 9/3/15 3:38 PM, "Tamas Nepusz" wrote: >Hi, > >There is no built-in function for this in igraph; you'll have to >implement the rewiring process yourself. > >T. >T. > > >On Thu, Sep 3, 2015 at 6:25 PM, Qunawei Zhang >wrote: >> Hello: >> >> I know how to use rewire and deSeq to randomize a network and keep the >> degree of the nodes. >> I have a protein-protein interaction network (192 nodes and 561 edges). >> Unlike other protein-protein interaction network, I found the >>interactions >> among hubs are not suppressed. I want to test whether this topology will >> make the subnetwork more vulnerable for random attacks. >> So I need some random network for comparison. To randomize the network >>I >> want to reduce the interactions among hub genes and on the other hand >> increase the number of interactions among hubs and non hubs. Is it >>possible >> to used some existing method in igraph to get this? >> >> Many thanks >> >> Best >> Quanwei >> >> >> >> ___ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> > >___ >igraph-help mailing list >igraph-help@nongnu.org >https://lists.nongnu.org/mailman/listinfo/igraph-help ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
Re: [igraph] randomize network with more controls
Hi, There is no built-in function for this in igraph; you'll have to implement the rewiring process yourself. T. T. On Thu, Sep 3, 2015 at 6:25 PM, Qunawei Zhang wrote: > Hello: > > I know how to use rewire and deSeq to randomize a network and keep the > degree of the nodes. > I have a protein-protein interaction network (192 nodes and 561 edges). > Unlike other protein-protein interaction network, I found the interactions > among hubs are not suppressed. I want to test whether this topology will > make the subnetwork more vulnerable for random attacks. > So I need some random network for comparison. To randomize the network I > want to reduce the interactions among hub genes and on the other hand > increase the number of interactions among hubs and non hubs. Is it possible > to used some existing method in igraph to get this? > > Many thanks > > Best > Quanwei > > > > ___ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help > ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
[igraph] randomize network with more controls
Hello: I know how to use rewire and deSeq to randomize a network and keep the degree of the nodes. I have a protein-protein interaction network (192 nodes and 561 edges). Unlike other protein-protein interaction network, I found the interactions among hubs are not suppressed. I want to test whether this topology will make the subnetwork more vulnerable for random attacks. So I need some random network for comparison. To randomize the network I want to reduce the interactions among hub genes and on the other hand increase the number of interactions among hubs and non hubs. Is it possible to used some existing method in igraph to get this? Many thanks Best Quanwei ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
Re: [igraph] ./configure won't detect GMP
Hi Tamas, I just figured it out. The problem was that I set CFLAGS but it seems I need to set CPPFLAGS instead. CFLAGS won't work. The reason why it seemed to work with MacPorts gmp is that actually I was using a MacPorts compiler at that time, which does look in /opt/local/include by default. On 3 September 2015 at 13:30, Tamas Nepusz wrote: > Hi Szabolcs, > > Can you send me the file named "configure.log" (to my private address)? > > T. > T. > > > On Thu, Sep 3, 2015 at 1:18 PM, Szabolcs Horvát wrote: >> Hi Tamas, >> >> Actually gmp.h is present in $HOME/local/include. I'm really confused >> about what is going wrong now. Maybe there's something obvious I'm >> missing? >> >> Witness: >> >> $ ls $HOME/local/include >> gmp.h igraph >> >> This is part of the output from ./configure: >> >> checking for libxml/parser.h... yes >> checking for __gmpz_add in -lgmp... yes >> checking gmp.h usability... no >> checking gmp.h presence... no >> checking for gmp.h... no >> checking that generated files are newer than configure... done >> >> So you are right that it doesn't find gmp.h >> >> But if I crudely remove the checking part from configure.ac and force >> it to try to use GMP anyway by setting gmp_support=yes, then igraph >> compiles without errors and works fine. >> >> On 2 September 2015 at 22:31, Tamas Nepusz wrote: >>> Hi Szabolcs, >>> >>> The configure script looks for a header named gmp.h and a library that >>> contains the symbol named __gmpz_add. I think that your LDFLAGS is >>> okay since it contains a .dylib or .so file that contains __gmpz_add, >>> but your CFLAGS variable should be like this: >>> >>> export CFLAGS=-I$HOME/local/include/gmp >>> >>> This is because gmp installs its headers in $prefix/include/gmp and >>> not in $prefix/include, and igraph tries to include them with #include >>> . >>> >>> T. >>> >>> T. >>> >>> >>> On Wed, Sep 2, 2015 at 5:54 PM, Szabolcs Horvát wrote: Dear All, I'm compiling igraph on OS X 10.10.5 using the system compiler. I'm trying to use GMP 6.0.0 from https://gmplib.org/, which I installed into $HOME/local. I configure igraph like this: export CFLAGS=-I$HOME/local/include export LDFLAGS=-L$HOME/local/lib ./configure --prefix=$HOME/local The configure script fails to detect GMP. How can I get it to succeed? Notes: It does detect MacPorts's GMP if I try to use it. It's also version 6.0.0. If I remove the part of the configure script that detects GMP to trick it into thinking that it's present, igraph does compile correctly, and it does work correctly (including functions that use GMP). I don't know anything about autoconf and don't understand how it tries to detect GMP ... Am I doing something wrong or is the GMP detection buggy? Szabolcs ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >>> ___ >>> igraph-help mailing list >>> igraph-help@nongnu.org >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> ___ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > ___ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
Re: [igraph] ./configure won't detect GMP
Hi Szabolcs, Can you send me the file named "configure.log" (to my private address)? T. T. On Thu, Sep 3, 2015 at 1:18 PM, Szabolcs Horvát wrote: > Hi Tamas, > > Actually gmp.h is present in $HOME/local/include. I'm really confused > about what is going wrong now. Maybe there's something obvious I'm > missing? > > Witness: > > $ ls $HOME/local/include > gmp.h igraph > > This is part of the output from ./configure: > > checking for libxml/parser.h... yes > checking for __gmpz_add in -lgmp... yes > checking gmp.h usability... no > checking gmp.h presence... no > checking for gmp.h... no > checking that generated files are newer than configure... done > > So you are right that it doesn't find gmp.h > > But if I crudely remove the checking part from configure.ac and force > it to try to use GMP anyway by setting gmp_support=yes, then igraph > compiles without errors and works fine. > > On 2 September 2015 at 22:31, Tamas Nepusz wrote: >> Hi Szabolcs, >> >> The configure script looks for a header named gmp.h and a library that >> contains the symbol named __gmpz_add. I think that your LDFLAGS is >> okay since it contains a .dylib or .so file that contains __gmpz_add, >> but your CFLAGS variable should be like this: >> >> export CFLAGS=-I$HOME/local/include/gmp >> >> This is because gmp installs its headers in $prefix/include/gmp and >> not in $prefix/include, and igraph tries to include them with #include >> . >> >> T. >> >> T. >> >> >> On Wed, Sep 2, 2015 at 5:54 PM, Szabolcs Horvát wrote: >>> Dear All, >>> >>> I'm compiling igraph on OS X 10.10.5 using the system compiler. >>> >>> I'm trying to use GMP 6.0.0 from https://gmplib.org/, which I >>> installed into $HOME/local. I configure igraph like this: >>> >>> export CFLAGS=-I$HOME/local/include >>> export LDFLAGS=-L$HOME/local/lib >>> ./configure --prefix=$HOME/local >>> >>> The configure script fails to detect GMP. How can I get it to succeed? >>> >>> Notes: It does detect MacPorts's GMP if I try to use it. It's also >>> version 6.0.0. If I remove the part of the configure script that >>> detects GMP to trick it into thinking that it's present, igraph does >>> compile correctly, and it does work correctly (including functions >>> that use GMP). >>> >>> I don't know anything about autoconf and don't understand how it tries >>> to detect GMP ... >>> >>> Am I doing something wrong or is the GMP detection buggy? >>> >>> Szabolcs >>> >>> ___ >>> igraph-help mailing list >>> igraph-help@nongnu.org >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> ___ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > ___ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
Re: [igraph] ./configure won't detect GMP
Hi Tamas, Actually gmp.h is present in $HOME/local/include. I'm really confused about what is going wrong now. Maybe there's something obvious I'm missing? Witness: $ ls $HOME/local/include gmp.h igraph This is part of the output from ./configure: checking for libxml/parser.h... yes checking for __gmpz_add in -lgmp... yes checking gmp.h usability... no checking gmp.h presence... no checking for gmp.h... no checking that generated files are newer than configure... done So you are right that it doesn't find gmp.h But if I crudely remove the checking part from configure.ac and force it to try to use GMP anyway by setting gmp_support=yes, then igraph compiles without errors and works fine. On 2 September 2015 at 22:31, Tamas Nepusz wrote: > Hi Szabolcs, > > The configure script looks for a header named gmp.h and a library that > contains the symbol named __gmpz_add. I think that your LDFLAGS is > okay since it contains a .dylib or .so file that contains __gmpz_add, > but your CFLAGS variable should be like this: > > export CFLAGS=-I$HOME/local/include/gmp > > This is because gmp installs its headers in $prefix/include/gmp and > not in $prefix/include, and igraph tries to include them with #include > . > > T. > > T. > > > On Wed, Sep 2, 2015 at 5:54 PM, Szabolcs Horvát wrote: >> Dear All, >> >> I'm compiling igraph on OS X 10.10.5 using the system compiler. >> >> I'm trying to use GMP 6.0.0 from https://gmplib.org/, which I >> installed into $HOME/local. I configure igraph like this: >> >> export CFLAGS=-I$HOME/local/include >> export LDFLAGS=-L$HOME/local/lib >> ./configure --prefix=$HOME/local >> >> The configure script fails to detect GMP. How can I get it to succeed? >> >> Notes: It does detect MacPorts's GMP if I try to use it. It's also >> version 6.0.0. If I remove the part of the configure script that >> detects GMP to trick it into thinking that it's present, igraph does >> compile correctly, and it does work correctly (including functions >> that use GMP). >> >> I don't know anything about autoconf and don't understand how it tries >> to detect GMP ... >> >> Am I doing something wrong or is the GMP detection buggy? >> >> Szabolcs >> >> ___ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > ___ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help ___ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
