Hello,
The code below is a hack.
First I create a layout ll, then see that vertex K coordinates are in
the layout matrix 2nd row.
Now, to multiply K's coordinates by a number d>1 will move the point
away from A. Add that value to the K group and plot.
ll <- layout_with_kk(my.graph)
d <- ll
Hi,
I was trying to make a network plot of this data:
library(igraph)
library(network)
df1 <- data.frame(from="A",to=c("B","C","D","E","F","G"),value=1)
df2 <- data.frame(from="K",to=c("L","M","N"),value=1)
df3 <- data.frame(from="A",to="K",value=3)
my.df <- rbind(df1,df2,df3)
my.g
Run this code
tree<-graph_from_literal(1-+2:3,3-+5,1-+4);
graph.bfs(tree,root=1, neimode="out",father=TRUE,order=TRUE,unreachable =
FALSE)
I do not understand why the father values will give NA 1 1 3 1 rather than NA
1 1 1 3
The reason I am doing this is to obtain the values(by vertex names) or
Dear all,
I am looking for a function to select the N closest neighbors (in terms of
distance) of a vertex in igraph.
Assume for example N=7. If the vertex has 3 direct neighbors, I would like
that the function selects those 3 plus a random 4 among the second degree
neighbors.
Is there some way
Loris Bennett writes:
> Hi,
>
> I am collecting data about network errors and would like to visualise
> the results in some sort of graph which reflects the hierarchy of the
> components in the network (i.e. core switches are connected to leaf
> switches and nodes are connected to leaf switches).
Hi,
I am collecting data about network errors and would like to visualise
the results in some sort of graph which reflects the hierarchy of the
components in the network (i.e. core switches are connected to leaf
switches and nodes are connected to leaf switches).
The errors are in file which look
Loris Bennett writes:
> Hi Jim,
>
> jim holtman writes:
>
>> Here is what it does locally on my PC:
>>
>>> library("igraph")
>>> topo_data <- read.table(text = "ibcore01ibswitch01
>> + ibcore01ibswitch02
>> + ibcore01ibswitch03
>> + ibcore02ibswitch01
>> + ib
Hi Jim,
jim holtman writes:
> Here is what it does locally on my PC:
>
>> library("igraph")
>> topo_data <- read.table(text = "ibcore01ibswitch01
> + ibcore01ibswitch02
> + ibcore01ibswitch03
> + ibcore02ibswitch01
> + ibcore02ibswitch02
> + ibcore02
Here is what it does locally on my PC:
> library("igraph")
> topo_data <- read.table(text = "ibcore01ibswitch01
+ ibcore01ibswitch02
+ ibcore01ibswitch03
+ ibcore02ibswitch01
+ ibcore02ibswitch02
+ ibcore02ibswitch03
+ ibswitch01 node001
Hi,
With the following data
ibcore01ibswitch01
ibcore01ibswitch02
ibcore01ibswitch03
ibcore02ibswitch01
ibcore02ibswitch02
ibcore02ibswitch03
ibswitch01 node001
ibswitch01 node002
ibswitch01 node003
ibswitch02 node004
ibswitch02
I wrote a simple script to build graphs:
require("RSQLite")
require('igraph')
drv <- dbDriver("SQLite")
con <- dbConnect(drv, "case.db")
dataset <- dbGetQuery(con, "select * from stream")
table <- aggregate(rep(1, nrow(dataset)), by = list(identifier =
dataset$actor_id, name = dataset$actor, page
recall. it's:
vertex.label.family
sorry
On 20 August 2013 17:30, Witold E Wolski wrote:
> Would like to plot vertex labels without serif.
> there is vertex.label.font param but he lets me choose only between
> one font type in normal bold and emph.
>
> any suggestions welcome.
>
>
> --
> Witold
Would like to plot vertex labels without serif.
there is vertex.label.font param but he lets me choose only between
one font type in normal bold and emph.
any suggestions welcome.
--
Witold Eryk Wolski
__
R-help@r-project.org mailing list
https://sta
Hi all,
I'm analysing an e-mail network. I loaded the following information in a
directed igraph:
*Vertex* types: person, e-mail
V(g)[ type == "person" ]
V(g)[ type == "email" ]
*Edge* types: sends, receives
E(g)[ type == "send" ]
E(g)[ type == "receive" ]
So for example:
John --send--> email1
On Tue, Aug 14, 2012 at 5:09 PM, Jonas Michaelis
wrote:
> Dear all,
>
>
> I have some network data - about 300 vertices and several thousand edges. I
> am looking for a way to turn multiple edges into weights of the edges. I
> looked around and - surprisingly? - haven't found anything. Is there an
On Wed, Aug 15, 2012 at 4:10 PM, Sam Steingold wrote:
[...]
> Also, this takes forever and consumes almost all 8GB RAM.
> It has been running on
>
> --8<---cut here---start->8---
> IGRAPH DNW- 18590 6734992 --
> + attr: name (v/c), count (v/n), weight (e/n)
> --
Hello,
There is a function count.multiple that can be used to do what you
want. You can also have a function return unique rows/edges. Here are
three functions that count multiple edges.
library(igraph)
ee <- c(1,2,2,3,1,2,2,4,1,2,2,3)
g <- graph(ee)
plot(g)
# Returns a two column matrix w
Dear all,
I have some network data - about 300 vertices and several thousand edges. I
am looking for a way to turn multiple edges into weights of the edges. I
looked around and - surprisingly? - haven't found anything. Is there an
easy way to do this?
Best, Jonas
[[alternative HTML ver
Hello R users,
I've just defended my PhD dissertation, and I'm engaging in discussions with
the "ruler lady". She has some problems with my figures. The problem is
that my nodes overlap the text that I've put inside of them.
Here is a url for the figure:
https://www.msu.edu/~wolfste4/igr
Marx
Cc: r-help@r-project.org
Subject: Re: [R] igraph function "graph.bfs" unavailable
Hi David,
please make sure that you have the 0.6 version of igraph installed.
You might need to upgrade your R installation to install the 0.6 version of
igraph.
Best,
Gabor
On Wed, Jul 11, 2012 a
Hi David,
please make sure that you have the 0.6 version of igraph installed.
You might need to upgrade your R installation to install the 0.6
version of igraph.
Best,
Gabor
On Wed, Jul 11, 2012 at 10:36 AM, David Marx wrote:
> Hi,
>
> I've installed the igraph package and have been otherwise u
Hi,
I've installed the igraph package and have been otherwise using it
successfully, but when I try to use graph.bfs I get the error:
could not find function "graph.bfs"
Moreover, I don't seem to have the documentation installed either. (per
?graph.bfs and ??graph.bfs).
I'm using RStudio
On Sat, Jun 2, 2012 at 9:58 AM, jalantho...@verizon.net
wrote:
> Could someone tell me the difference between igraph and igraph0?
>
> I searched the CRAN web site, but cannot find an explantion of the
> differences.
You are right that this should be in the package description.
There is no diffe
Could someone tell me the difference between igraph and igraph0?
I searched the CRAN web site, but cannot find an explantion of the differences.
Thanks, Alan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://st
On 12-03-20 2:20 PM, Sam Steingold wrote:
I just got this error:
library(igraph)
comp<- decompose.graph(gr)
Error: protect(): protection stack overflow
Error: protect(): protection stack overflow
what can I do?
the digraph is, indeed, large (300,000 vertexes), but there are very
many very s
> * Sam Steingold [2012-03-20 14:20:06 -0400]:
>
> I just got this error:
>> library(igraph)
>> comp <- decompose.graph(gr)
> Error: protect(): protection stack overflow
> Error: protect(): protection stack overflow
>>
after restarting
> system.time(comp <- decompose.graph(gr, mode="weak"))
Err
I just got this error:
> library(igraph)
> comp <- decompose.graph(gr)
Error: protect(): protection stack overflow
Error: protect(): protection stack overflow
>
what can I do?
the digraph is, indeed, large (300,000 vertexes), but there are very
many very small components (which I would rather not
Hi all,
I am trying to analyze some graphs in R. Given a weighted directed network
with 7 nodes. I want to find a path from node 1 to node 7, so the sum of all
the edges on the path is the smallest comparing to all the other paths. I am
wondering if I can do this in igraph. After I identify the p
Hi List,
I have a set of small graphs with weighted and directed edges (< 40 vertices
each).
As igraph's 'transitivity' function ignores the edge weight & direction, I
wonder if there's any method for estimating the global clustering
coefficient for such graphs..?
Cheers,
Tom
--
View this me
Create a factor variable for the different age categories, see cut().
Then use as.integer() on the factor variable and index a vector of
node sizes with it. E.g.
g <- graph.ring(10)
V(g)$age <- sample(20:78, vcount(g), replace=TRUE)
V(g)$agecat <- cut(V(g)$age, breaks = c(20,35,50,65,78))
V(g)$siz
Hi,
I'm working on some social networks and I managed to create the graphs with
labels and edges weight, but I would also like to change the size of the
vertices according to the age of the persons in the network and the shape
according to the gender. Now for the age, I have people with ages be
Dear R users,
I'm using igraph package for clustering, just wondering is
leading.eigenvector.community function result deterministic or not?
I got slightly different results on different runs...
Many thanks
Yan
***
Hi to all,
I have two graphs with the same number of nodes but with different
connectivities and also with a different number of clusters.
The two graphs represent the same "system" under different "conditions" and
then there is a one-to-one correspondence between a given node in the two
graphs.
I
Dear all,
I'm doing some experiments with igraph and in particular with graph layouts.
I can't figure out how to apply a layout to a given (real) graph avoiding
node overlaps.
In the following example if the variable NumOfNodes is setted to a small
value (10) the
layout function generates a plot
Hi
gabrielap wrote:
Hello...
I am a system engeenering student and I am using R for first time for
Graph Theory. I would like to know if there is anyway you can plot an ghaph
(igraph library) and obtain a graph whose vertices dont appear identified
with number, instead I would like the ve
Hello...
I am a system engeenering student and I am using R for first time for
Graph Theory. I would like to know if there is anyway you can plot an ghaph
(igraph library) and obtain a graph whose vertices dont appear identified
with number, instead I would like the vertices to be identified
On Sun, Dec 06, 2009 at 04:34:18PM -0800, Brock Tibert wrote:
> I have successfully created and analyzed my network data. I am
> new to R, and Network Analysis too, but I want to color my
> vertex based on some of the centrality measures calculated.
>
> Can someone point me in the right directi
Hi everyone,
I have successfully created and analyzed my network data. I am new to R, and
Network Analysis too, but I want to color my vertex based on some of the
centrality measures calculated.
Can someone point me in the right direction? Again, I am new to R, but given
how powerful R appe
Hi,
On Fri, Dec 4, 2009 at 3:12 AM, Gaurav Kumar wrote:
> Hi R-users,
>
> I'm using igraph for an undirected graph.
> i used clusters() igraph function to know the component size(subgraphs) as
> shown bellow:
> c <-clusters(g)
> # component sizes
> size <- sort(c$csize, decreasing=TRUE)
> cat("T
Hi R-users,
I'm using igraph for an undirected graph.
i used clusters() igraph function to know the component size(subgraphs) as
shown bellow:
c <-clusters(g)
# component sizes
size <- sort(c$csize, decreasing=TRUE)
cat("Top 20 cluster of the graph","\n")
for (i in 1:20)
{
cat(i," size:",s
Knut, see this thread here:
http://lists.gnu.org/archive/html/igraph-help/2007-07/msg00010.html
Best,
Gabor
On Thu, Apr 16, 2009 at 10:03 AM, Knut Krueger wrote:
> Does anybody know how to solve this error?
>
> postscript(file= "file.ps", family = "Helvetica", font = "Helvetica")
> plot.igraph(g
Does anybody know how to solve this error?
postscript(file= "file.ps", family = "Helvetica", font = "Helvetica")
plot.igraph(g, layout=layout.circle, vertex.label.font=2)
dev.off()
error in text.default(x, y, labels = labels, col = label.color, family
= label.family, :
family 'serif' not inc
Yep, this is a bug, thanks for reporting it. It only happens with the
square shape, so until it is a corrected, a workaround is using
"rectangle" shape, with equal vertical and horizontal sizes:
g <- graph.ring(4)
g$layout <- layout.circle
V(g)$size <- seq_len(vcount(g)) * 10
V(g)$size2 <- V(g)$si
When the shape of all vertices is set to "square" and the size of the vertices
is also set, one get following error (commands attached):
Error in l[[which.min(sapply(l, function(p) (p[1] - x0)^2 + (p[2] - y0)^2))]] :
attempt to select less than one element
Is there a way to solve this pr
Rainer,
here is a quick workaround:
layout.svd3 <- function (graph, d = shortest.paths(graph), ...)
{
if (!is.igraph(graph)) {
stop("Not a graph object")
}
l <- svd(d, 3)$u
l[, 1] <- l[, 1]/dist(range(l[, 1]))
l[, 2] <- l[, 2]/dist(range(l[, 2]))
l[, 3] <- l[, 3]/dist(range(l[, 3]
The layout.svd-function in the igraph-package seems to support only
two-dimensional layouts currently. Is anybody aware of a workaround to obtain
the coordinate-values for the third dimension? (And by the way, is it possible
to change the background-color in rglplots?)
I'm using the R-2.6.2 vers
On Sun, Nov 16, 2008 at 7:14 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
> Gábor Csárdi wrote:
>>
>> On Sun, Nov 16, 2008 at 3:01 PM, Gábor Csárdi <[EMAIL PROTECTED]>
>> wrote:
>>>
>>> Tom,
>>>
>>> On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]>
>>> wrote:
>>
>> [...]
Gábor Csárdi wrote:
On Sun, Nov 16, 2008 at 3:01 PM, Gábor Csárdi <[EMAIL PROTECTED]> wrote:
Tom,
On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
[...]
suspicion that if the relations between two vertices is non-symmetric, only
one of the is shown. Is it possib
Gábor Csárdi wrote:
On Sun, Nov 16, 2008 at 3:01 PM, Gábor Csárdi <[EMAIL PROTECTED]> wrote:
Tom,
On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
[...]
suspicion that if the relations between two vertices is non-symmetric, only
one of the is shown. Is it possib
Gábor Csárdi wrote:
Tom,
On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
Gabor:
Actually, I meant a script GUI management of ugraph I managed to locate on
the net.
Oh, ok, it will be part of igraph from the next version. But its
capabilities are very limited. W
On Sun, Nov 16, 2008 at 3:01 PM, Gábor Csárdi <[EMAIL PROTECTED]> wrote:
> Tom,
>
> On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
[...]
>> suspicion that if the relations between two vertices is non-symmetric, only
>> one of the is shown. Is it possible to have a p
Tom,
On Fri, Nov 14, 2008 at 4:35 PM, Tom Backer Johnsen <[EMAIL PROTECTED]> wrote:
> Gabor:
>
> Actually, I meant a script GUI management of ugraph I managed to locate on
> the net.
Oh, ok, it will be part of igraph from the next version. But its
capabilities are very limited. We are considering
Gabor:
Actually, I meant a script GUI management of ugraph I managed to locate
on the net. Disregarding that, thank you for the suggestions. igraph
is definitly a non-trivial affair, with a lot of options and
corresponding flexibility. I made some changes to what you wrote:
A <- matrix(sa
Tom, you mean 'tkplot' in the igraph package? Look at ?igraph.plotting
on how to set up plotting parameters, e.g. if you want different line
types for the positive/negative relations, then you can make use of
the 'lty' parameter:
A <- matrix(sample(c(-1,0,1), 100, replace=TRUE), 10)
g <- graph.adj
I have a number of (directed) graphs based on social groups, where the
members have expresed likes and dislikes in respect to the other
members. tkgraph makes it simple to draw the graphs in a very pleasing
way, but I would like to differentiate between positive and negative
relations in the g
rote:
>
> > From: Moshe Olshansky <[EMAIL PROTECTED]>
> > Subject: Re: [R] Igraph library: How to calculate APSP (shortest path
> > matrix) matrix for a subset list of nodes.
> > To: r-help@r-project.org, "dinesh kumar" <[EMAIL PROTECTED]>
> &g
I was too optimistic - the complexity is O(E*log(V)) where V is the number of
nodes, but since log(25000) < 20 this is still reasonable.
--- On Mon, 25/8/08, Moshe Olshansky <[EMAIL PROTECTED]> wrote:
> From: Moshe Olshansky <[EMAIL PROTECTED]>
> Subject: Re: [R] I
require about
100,000*500 = 50,000,000 operations (times a small factor) which is very
reasonable.
--- On Mon, 25/8/08, dinesh kumar <[EMAIL PROTECTED]> wrote:
> From: dinesh kumar <[EMAIL PROTECTED]>
> Subject: [R] Igraph library: How to calculate APSP (shortest path matri
Dear R Users,
I have a network of 25000 total nodes and a list of 500 node which is a
subset of all nodes. Now I want to calculate the APSP (all pair shortest
path) matrix only for these 500 nodes.
I would appreciate any help.
Thanks in advance
Dinesh
--
Dinesh Kumar Barupal
Research Associate
Wanding,
I'm the maintainer of igraph, but missed your previous email.
Yes, currently the released version of igraph fails to compile
with gcc 4.3.x. I made the required modifications to fix this,
but these are still in the igraph development tree, as there has been
no release since that.
Yo
Please discuss this with the package maintainer (see the posting guide).
He will need lots of details you have omitted, including the precise OS
and the C++ compiler used.
BTW, this illustrates a common problem with packages using C++, which
people often test only under one compiler, and unti
Dieter,
there are a couple of ways to do this in igraph, eg.
you can decompose the graph into separate components with
g <- erdos.renyi.game(100, 1/100)
graphs <- decompose.graph(g)
and then you will have a list of graphs. If you assign some vertex
ids as vertex attributes then you can keep tra
On Mon, Oct 08, 2007 at 08:11:16PM -0500, [EMAIL PROTECTED] wrote:
[...]
> Dot-file format is also *ridiculously simple* to generate , which I think
> of as a factor well in its favor. :-)
This is just
write.graph(g, format="dot", file="output.dot")
in igraph.
> I hear that there's a tk-based
>> Hello there,
>>
>> I am using the igraph package to build graphs from my data. If I plot
>> a graph though, it's not easy for me to see what's going on. Does
>> anybody know how to rearrange a graph to get a plot without too many
>> crossing lines? Maybe other packages?
Edge-crossing mi
On 08/10/2007 8:27 PM, Dieter Best wrote:
> Hello there,
>
> I am using the igraph package to build graphs from my data. If I plot a
> graph though, it's not easy for me to see what's going on. Does anybody know
> how to rearrange a graph to get a plot without too many crossing lines? Maybe
graph, RBGL and Rgraphviz, all available at www.bioconductor.org
Dieter Best wrote:
> Hello there,
>
> I am using the igraph package to build graphs from my data. If I plot a
> graph though, it's not easy for me to see what's going on. Does anybody know
> how to rearrange a graph to get a
Hello there,
I am using the igraph package to build graphs from my data. If I plot a graph
though, it's not easy for me to see what's going on. Does anybody know how to
rearrange a graph to get a plot without too many crossing lines? Maybe other
packages?
Thanks a lot in advance for
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