[igraph] Derived layouts for subgraphs

[David Edwards]

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
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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 <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] plotting graphs with edges of various length
Message-ID:
        <address@hidden>
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 <address@hidden> 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
>
>
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Message: 2
Date: Sun, 9 Mar 2014 20:32:15 +0100
From: Tam?s Nepusz <address@hidden>
To: Help for igraph users <address@hidden>, aschmid1
        <address@hidden>
Subject: Re: [igraph] plotting graphs with edges of various length
Message-ID: <address@hidden>
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 <address@hidden>
To: Tam?s Nepusz <address@hidden>
Cc: Help for igraph users <address@hidden>
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 <address@hidden>
To: Help for igraph users <address@hidden>
Cc: Tam?s Nepusz <address@hidden>
Subject: Re: [igraph] plotting graphs with edges of various length
Message-ID:
        <address@hidden>
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 <address@hidden> 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
>
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Message: 5
Date: Sun, 9 Mar 2014 19:46:26 -0500
From: David Gelvez Alvarez <address@hidden>
To: address@hidden
Subject: [igraph] Installation error
Message-ID:
        <address@hidden>
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 <igraph_arpack.h>
         ^
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
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Message: 6
Date: Sun, 9 Mar 2014 21:15:23 -0400
From: G?bor Cs?rdi <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] Installation error
Message-ID:
        <address@hidden>
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
<address@hidden>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 <igraph_arpack.h>
>          ^
> 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
>
>
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Message: 7
Date: Mon, 10 Mar 2014 11:09:12 +0100
From: Tam?s Nepusz <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] Installation error
Message-ID: <address@hidden>
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 <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] Installation error
Message-ID: <address@hidden>
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 <address@hidden>
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] Installation error
Message-ID:
        <address@hidden>
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 <igraph_arpack.h>
         ^
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 <address@hidden> 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
>
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