|
| From: | Gábor Csárdi |
| Subject: | Re: [igraph] Derived layouts for subgraphs |
| Date: | Tue, 11 Mar 2014 09:23:01 -0400 |
Hi,
Your request makes perfect sense but there are a few corner cases that should be taken into consideration:
1) layouts are not “associated” to the graph they are created from so they cannot “detect” when the graph is subsetted
2) even if layouts were associated to a graph, it is entirely possible to work with two separate layouts for the same graph, in which case it would be unclear which layout is the one that should be assigned to the induced subgraph.
Actually, you can also assign a layout to a graph by setting the “layout” attribute of the graph as follows:
g$layout <- layout.fruchterman.reingold(g)
I think that it would be useful if induced.subgraph() could also update the $layout attribute of the subgraph based on the $layout attribute of the original graph; I leave it up to Gabor to decide whether he wants to implement it in the R interface or not.
Reply: David Edwards address@hidden
Date: 11 March 2014 at 10:36:41
To: Tamás Nepusz address@hidden
Subject: RE: [igraph] Derived layouts for subgraphs
> Hi,
>
> Thanks for this. No, its not because its a difficult problem for a user to deal with, I just
> thought that it would be nice if it was default.
>
> Regards
> David
>
>
>
> ________________________________________
> From: Tamás Nepusz [address@hidden]
> Sent: 11 March 2014 10:20
> To: David Edwards; Help for igraph users
> Subject: Re: [igraph] Derived layouts for subgraphs
>
> Hi,
>
> The layout of a graph is simply a matrix with n rows and 2 columns, so one thing that you can
> do is to store the layout separately and then subset the matrix for the individual subgraphs;
> e.g.:
>
> layout <- layout.fruchterman.reingold(g)
> subg <- induced.subgraph(g, vids)
> sublayout <- layout[vids,]
> plot(subg, layout=sublayout)
>
> Another option is to store the X and Y coordinates of the layout in vertex attributes named
> “x” and “y”, because these are used automatically by igraph when you plot a graph:
>
> layout <- layout.fruchterman.reingold(g)
> V(g)$x <- layout[,1]
> V(g)$y <- layout[,2]
> subg <- induced.subgraph(g, vids)
> plot(subg)
>
> --
> T.
>
> ------------------------------------------------------
> From: David Edwards address@hidden
> Reply: Help for igraph users address@hidden
> Date: 11 March 2014 at 08:24:21
> To: address@hidden address@hidden
> Subject: [igraph] Derived layouts for subgraphs
>
> > Hi
> > when the layout of graph G is set, could
> > induced.subgraph(G, vids) (for some vector vids of vertex ids)
> > inherit that layout? (it seems to inherit other attributes).
> > Best regards
> > David
> > ________________________________________
> > From: igraph-help-bounces+david.edwards=address@hidden [igraph-help-bounces+david.edwards=address@hidden]
> > on behalf of address@hidden [address@hidden]
> > Sent: 10 March 2014 17:01
> > To: address@hidden
> > Subject: igraph-help Digest, Vol 92, Issue 6
> >
> > Send igraph-help mailing list submissions to
> > address@hidden
> >
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> > When replying, please edit your Subject line so it is more specific
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> >
> >
> > Today's Topics:
> >
> > 1. Re: plotting graphs with edges of various length (G?bor Cs?rdi)
> > 2. Re: plotting graphs with edges of various length (Tam?s Nepusz)
> > 3. Re: plotting graphs with edges of various length (aschmid1)
> > 4. Re: plotting graphs with edges of various length (G?bor Cs?rdi)
> > 5. Installation error (David Gelvez Alvarez)
> > 6. Re: Installation error (G?bor Cs?rdi)
> > 7. Re: Installation error (Tam?s Nepusz)
> > 8. Re: Installation error (Tam?s Nepusz)
> > 9. Re: Installation error (David Gelvez Alvarez)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 9 Mar 2014 14:38:47 -0400
> > From: G?bor Cs?rdi
> > To: Help for igraph users
> > Subject: Re: [igraph] plotting graphs with edges of various length
> > Message-ID:
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi, maybe I am missing something, but what is your question?
> >
> > Why some red edges are shorter? For that we would need a reproducible
> > example.
> >
> > Why the "weight" and/or "length" attribute is not used automatically? Or
> > something else?
> >
> > Gabor
> >
> >
> > On Sat, Mar 8, 2014 at 10:37 PM, aschmid1 wrote:
> >
> > > Hi,
> > > I thought that the commands
> > > gm<-set.edge.attribute(gm, "weight", index=E(gm), value=weights)
> > > gm<-set.edge.attribute(gm, "length", index=E(gm), value=weights)
> > > ensure that plot(gm) yields the edge lengths corresponding to the values
> > > of vector weights. It seems not the case. I attach the graph in which blue
> > > edges have weights < 1 and red edges have weights >1. However, some red
> > > edges look shorter than some blue edges.
> > > Thanks much, Alec
> > > _______________________________________________
> > > igraph-help mailing list
> > > address@hidden
> > > https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 9 Mar 2014 20:32:15 +0100
> > From: Tam?s Nepusz
> > To: Help for igraph users , aschmid1
> >
> > Subject: Re: [igraph] plotting graphs with edges of various length
> > Message-ID:
> > Content-Type: text/plain; charset="utf-8"
> >
> > > I thought that the commands
> > > gm<-set.edge.attribute(gm, "weight", index=E(gm), value=weights)
> > > gm<-set.edge.attribute(gm, "length", index=E(gm), value=weights)
> > > ensure that plot(gm) yields the edge lengths corresponding to the values
> > > of vector weights.
> > No, it doesn?t. *Some* layout algorithms *might* take into account the weights of the
> > edges to *some* extent (i.e. they would *try* to ensure that edges with larger weights
> > end up being shorter than edges with smaller weights), but there is no layout algorithm
> > that would guarantee that the lengths you specify are satisfied exactly. The main reason
> > is that most of the length combinations are impossible to satisfy in the 2D plane; for
> > instance, it is impossible to plot a full graph of size 4 if we want every single edge to
> > be of length 1 (and there are infinitely many examples for this).
> >
> > As far as I know, the Fruchterman-Reingold layout algorithm (see layout.fruchterman.reingold)
> > is the only one in igraph that supports weights; see?http://igraph.sourceforge.net/doc/R/layout.html
> > . But even for the Fruchterman-Reingold algorithm, the only thing that the weights
> do
> > is that they make the attraction forces between the endpoints of the edges proportional
> > to the weight of the edge.
> >
> > ??
> > T.
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Sun, 09 Mar 2014 18:05:37 -0400
> > From: aschmid1
> > To: Tam?s Nepusz
> > Cc: Help for igraph users
> > Subject: Re: [igraph] plotting graphs with edges of various length
> > Message-ID: <address@hidden>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > Tamas,
> > Thank you. I suspected I wanted too much from igraph. Indeed one cannot
> > draw say a triangle with arbitrary edge lengths... But then I have a
> > naive question (I'm new to graphs): how the edge attribute "length" may
> > be used (providing there is also attribute "weight")?
> > Best, Alec
> >
> > On 03/09/2014 3:32 PM, Tam?s Nepusz wrote:
> > >> I thought that the commands
> > >> gm<-set.edge.attribute(gm, "weight", index=E(gm), value=weights)
> > >> gm<-set.edge.attribute(gm, "length", index=E(gm), value=weights)
> > >> ensure that plot(gm) yields the edge lengths corresponding to the
> > >> values
> > >> of vector weights.
> > > No, it doesn?t. *Some* layout algorithms *might* take into account the
> > > weights of the edges to *some* extent (i.e. they would *try* to ensure
> > > that edges with larger weights end up being shorter than edges with
> > > smaller weights), but there is no layout algorithm that would
> > > guarantee that the lengths you specify are satisfied exactly. The main
> > > reason is that most of the length combinations are impossible to
> > > satisfy in the 2D plane; for instance, it is impossible to plot a full
> > > graph of size 4 if we want every single edge to be of length 1 (and
> > > there are infinitely many examples for this).
> > >
> > > As far as I know, the Fruchterman-Reingold layout algorithm (see
> > > layout.fruchterman.reingold) is the only one in igraph that supports
> > > weights; see?http://igraph.sourceforge.net/doc/R/layout.html . But
> > > even for the Fruchterman-Reingold algorithm, the only thing that the
> > > weights do is that they make the attraction forces between the
> > > endpoints of the edges proportional to the weight of the edge.
> > >
> > > ??
> > > T.
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Sun, 9 Mar 2014 19:01:09 -0400
> > From: G?bor Cs?rdi
> > To: Help for igraph users
> > Cc: Tam?s Nepusz
> > Subject: Re: [igraph] plotting graphs with edges of various length
> > Message-ID:
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > I am not sure why you think the "length" edge attribute is used for
> > anything. It is not, AFAIK.
> >
> > G.
> >
> >
> > On Sun, Mar 9, 2014 at 6:05 PM, aschmid1 wrote:
> >
> > > Tamas,
> > > Thank you. I suspected I wanted too much from igraph. Indeed one cannot
> > > draw say a triangle with arbitrary edge lengths... But then I have a naive
> > > question (I'm new to graphs): how the edge attribute "length" may be used
> > > (providing there is also attribute "weight")?
> > > Best, Alec
> > >
> > >
> > > On 03/09/2014 3:32 PM, Tam?s Nepusz wrote:
> > >
> > >> I thought that the commands
> > >>> gm<-set.edge.attribute(gm, "weight", index=E(gm), value=weights)
> > >>> gm<-set.edge.attribute(gm, "length", index=E(gm), value=weights)
> > >>> ensure that plot(gm) yields the edge lengths corresponding to the values
> > >>> of vector weights.
> > >>>
> > >> No, it doesn't. *Some* layout algorithms *might* take into account the
> > >> weights of the edges to *some* extent (i.e. they would *try* to ensure
> > >> that edges with larger weights end up being shorter than edges with
> > >> smaller weights), but there is no layout algorithm that would
> > >> guarantee that the lengths you specify are satisfied exactly. The main
> > >> reason is that most of the length combinations are impossible to
> > >> satisfy in the 2D plane; for instance, it is impossible to plot a full
> > >> graph of size 4 if we want every single edge to be of length 1 (and
> > >> there are infinitely many examples for this).
> > >>
> > >> As far as I know, the Fruchterman-Reingold layout algorithm (see
> > >> layout.fruchterman.reingold) is the only one in igraph that supports
> > >> weights; see http://igraph.sourceforge.net/doc/R/layout.html . But
> > >> even for the Fruchterman-Reingold algorithm, the only thing that the
> > >> weights do is that they make the attraction forces between the
> > >> endpoints of the edges proportional to the weight of the edge.
> > >>
> > >> --
> > >> T.
> > >>
> > >
> > > _______________________________________________
> > > igraph-help mailing list
> > > address@hidden
> > > https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Sun, 9 Mar 2014 19:46:26 -0500
> > From: David Gelvez Alvarez
> > To: address@hidden
> > Subject: [igraph] Installation error
> > Message-ID:
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear all,
> >
> > Thanks a lot for your help. I'm trying to install igraph for python but I
> > have not been able to do it. I have the Anaconda Python version.
> >
> > I downloaded the dmg for the 0.7 version and followed the dialog and the
> > import does not work. Also, I tried to use the easy install and I get the
> > following error:
> >
> > In file included from src/arpackobject.c:23:
> > src/arpackobject.h:27:10: fatal error: 'igraph_arpack.h' file not found
> > #include
> > ^
> > 1 error generated.
> > error: Setup script exited with error: command 'gcc' failed with exit
> > status 1
> >
> > Can some one give me a hand?
> >
> > Kind regards,
> >
> > David
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Sun, 9 Mar 2014 21:15:23 -0400
> > From: G?bor Cs?rdi
> > To: Help for igraph users
> > Subject: Re: [igraph] Installation error
> > Message-ID:
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi, the DMG is for the system python, so it won't work with Anaconda
> > (apparently).
> >
> > If you install from source you need to install the igraph C library first.
> >
> > Gabor
> >
> >
> > On Sun, Mar 9, 2014 at 8:46 PM, David Gelvez Alvarez
> > wrote:
> >
> > > Dear all,
> > >
> > > Thanks a lot for your help. I'm trying to install igraph for python but I
> > > have not been able to do it. I have the Anaconda Python version.
> > >
> > > I downloaded the dmg for the 0.7 version and followed the dialog and the
> > > import does not work. Also, I tried to use the easy install and I get the
> > > following error:
> > >
> > > In file included from src/arpackobject.c:23:
> > > src/arpackobject.h:27:10: fatal error: 'igraph_arpack.h' file not found
> > > #include
> > > ^
> > > 1 error generated.
> > > error: Setup script exited with error: command 'gcc' failed with exit
> > > status 1
> > >
> > > Can some one give me a hand?
> > >
> > > Kind regards,
> > >
> > > David
> > >
> > > _______________________________________________
> > > igraph-help mailing list
> > > address@hidden
> > > https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Mon, 10 Mar 2014 11:09:12 +0100
> > From: Tam?s Nepusz
> > To: Help for igraph users
> > Subject: Re: [igraph] Installation error
> > Message-ID:
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello,
> >
> > As Gabor has confirmed it, the DMG won?t work because it installs igraph for the system
> > Python (that comes built-in with Mac OS X) and not Anaconda Python. You have to compile
> > the Python module yourself. easy_installing python-igraph does not work yet because
> > you have not downloaded and installed the C core of igraph, and the Python interface
> depends
> > on the C core.
> >
> > Actually, I was a bit lazy as I haven?t released the 0.7 version of the Python interface
> > yet even though the core C library is already at version 0.7. Let me release the 0.7 version
> > first (I?ll do it today) and then you can retry with easy_install because the installer
> > of the 0.7 version should now be smart enough to download and compile the corresponding
> > C library as well if you have not installed it already.
> >
> > All the best,
> > --
> > T.
> >
> > ------------------------------------------------------
> > From:?David Gelvez Alvarez address@hidden
> > Reply:?Help for igraph users address@hidden
> > Date:?10 March 2014 at 01:47:20
> > To:?address@hidden address@hidden
> > Subject:? [igraph] Installation error
> >
> > > Dear all,
> > >
> > > Thanks a lot for your help. I'm trying to install igraph for python but I
> > > have not been able to do it. I have the Anaconda Python version.
> > >
> > > I downloaded the dmg for the 0.7 version and followed the dialog and the
> > > import does not work. Also, I tried to use the easy install and I get the
> > > following error:
> > >
> > > In file included from src/arpackobject.c:23:
> > > src/arpackobject.h:27:10: fatal error: 'igraph_arpack.h' file not found
> > > #include
> > > ^
> > > 1 error generated.
> > > error: Setup script exited with error: command 'gcc' failed with exit
> > > status 1
> > >
> > > Can some one give me a hand?
> > >
> > > Kind regards,
> > >
> > > David
> > > _______________________________________________
> > > igraph-help mailing list
> > > address@hidden
> > > https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Mon, 10 Mar 2014 11:20:57 +0100
> > From: Tam?s Nepusz
> > To: Help for igraph users
> > Subject: Re: [igraph] Installation error
> > Message-ID:
> > Content-Type: text/plain; charset="utf-8"
> >
> > > Actually, I was a bit lazy as I haven?t released the 0.7 version of the Python interface?
> > > yet even though the core C library is already at version 0.7. Let me release the 0.7 version
> > > first (I?ll do it today)
> > Okay, it turned out to be faster than expected; the source code of the Python interface
> > for the 0.7 version is now uploaded to the Python Package Index. I tried ?easy_install
> > python-igraph? in a clean virtual environment on a machine where the C core was not installed
> > and everything went fine, so please try ?easy_install python-igraph? again and let
> > me know if it does not work with Anaconda Python.
> >
> > All the best,
> > Tamas
> >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Mon, 10 Mar 2014 05:58:38 -0500
> > From: David Gelvez Alvarez
> > To: Help for igraph users
> > Subject: Re: [igraph] Installation error
> > Message-ID:
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi All,
> >
> > Thank you for your prompt answer. I tried the easy install, but here is
> > what I get. Thanks again for your help!
> >
> > David
> >
> > *********** Log starts here
> >
> > grep: /usr/lib/libiconv.la: No such file or directory
> > sed: /usr/lib/libiconv.la: No such file or directory
> > libtool: link: `/usr/lib/libiconv.la' is not a valid libtool archive
> > make[3]: *** [libigraph.la] Error 1
> > make[2]: *** [all] Error 2
> > make[1]: *** [all-recursive] Error 1
> > make: *** [all] Error 2
> > Could not download and compile the C core of igraph.
> >
> > WARNING: we were not able to detect where igraph is installed on
> > your machine (if it is installed at all). We will use the fallback
> > library and include pathss hardcoded in setup.py and hope that the
> > C core of igraph is installed there.
> >
> > If the compilation fails and you are sure that igraph is installed
> > on your machine, adjust the following two variables in setup.py
> > accordingly and try again:
> >
> > - LIBIGRAPH_FALLBACK_INCLUDE_DIRS
> > - LIBIGRAPH_FALLBACK_LIBRARY_DIRS
> >
> > Build type: dynamic extension
> > Include path: /usr/include/igraph /usr/local/include/igraph
> > Library path:
> > Linked dynamic libraries: igraph
> > Linked static libraries:
> > Extra compiler options:
> > Extra linker options:
> > In file included from src/arpackobject.c:23:
> > src/arpackobject.h:27:10: fatal error: 'igraph_arpack.h' file not found
> > #include
> > ^
> > 1 error generated.
> > error: Setup script exited with error: command 'gcc' failed with exit
> > status 1
> >
> >
> > On Mon, Mar 10, 2014 at 5:20 AM, Tam?s Nepusz wrote:
> >
> > > > Actually, I was a bit lazy as I haven't released the 0.7 version of the
> > > Python interface
> > > > yet even though the core C library is already at version 0.7. Let me
> > > release the 0.7 version
> > > > first (I'll do it today)
> > > Okay, it turned out to be faster than expected; the source code of the
> > > Python interface for the 0.7 version is now uploaded to the Python Package
> > > Index. I tried "easy_install python-igraph" in a clean virtual environment
> > > on a machine where the C core was not installed and everything went fine,
> > > so please try "easy_install python-igraph" again and let me know if it does
> > > not work with Anaconda Python.
> > >
> > > All the best,
> > > Tamas
> > >
> > > _______________________________________________
> > > igraph-help mailing list
> > > address@hidden
> > > https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> > ------------------------------
> >
> > _______________________________________________
> > igraph-help mailing list
> > address@hidden
> > https://lists.nongnu.org/mailman/listinfo/igraph-help
> >
> >
> > End of igraph-help Digest, Vol 92, Issue 6
> > ******************************************
> >
> > _______________________________________________
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> >
>
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