Rgraphviz doesn't seem to handle edge weights

[january3]

Edge weights are important for layouts such as neato and fdp, but do not seem to be imported by Rgraphviz agopen() function. Graphs produced using the fdp layout, even if edges have different weights, have always the same edge length. Example:

graph <- new( "graphNEL", nodes= LETTERS[1:5], edgemode="undirected" )
graph <- addEdge( rep( "A", 4 ), LETTERS[2:5], graph, weights= 10^c( 1, 2, 3, 4 ) )
rag <- agopen( graph, "", layoutType= "fdp" )
plot(rag)

Compare with the equivalent graph produced from the following .dot file using the command fdp -Tpng example.dot -o example.png

digraph { 
  node [shape=ellipse];  
  // nodes
  A B C D E;
  // labelled, weighted edges
  A -> B[weight="0.1"];
  A -> C[weight="10"]; 
  A -> D[weight="100"]; 
  A -> E[weight="1000"]; 
}

[kasperdanielhansen]

This looks like a bug. However, I have to point out that the two graphs are not identical - one is undirected, the other is not and the edge weights are slightly different. I don't know enough about the internals of fdp to know if this makes a difference, but it should be easy to test.

Nevertheless I do think it looks like a bug.

Just for the record: which version of Graphviz did you use for the command line example?

[january3]

Hi Kasper, version 2.8.1

here is my sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods
base

other attached packages:
[1] Rgraphviz_2.8.1 graph_1.42.0 tmod_0.9 pca3d_0.4
myfuncs_1.5 setwidth_1.0-3 colorout_0.9-9

loaded via a namespace (and not attached):
[1] beeswarm_0.1.6 BiocGenerics_0.10.0 igraph_0.7.1
parallel_3.1.2 rgl_0.95.1201 stats4_3.1.2 tools_3.1.2

On 27 March 2015 at 18:47, Kasper Daniel Hansen [email protected]
wrote:

This looks like a bug. However, I have to point out that the two graphs
are not identical - one is undirected, the other is not and the edge
weights are slightly different. I don't know enough about the internals of
fdp to know if this makes a difference, but it should be easy to test.

Nevertheless I do think it looks like a bug.

Just for the record: which version of Graphviz did you use for the command
line example?

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-------- January Weiner --------------------------------------

[kasperdanielhansen]

I meant command-line graphviz;, just do

fdp -V

Kasper

On Fri, Mar 27, 2015 at 2:47 PM, january3 [email protected] wrote:

Hi Kasper, version 2.8.1

here is my sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods
base

other attached packages:
[1] Rgraphviz_2.8.1 graph_1.42.0 tmod_0.9 pca3d_0.4
myfuncs_1.5 setwidth_1.0-3 colorout_0.9-9

loaded via a namespace (and not attached):
[1] beeswarm_0.1.6 BiocGenerics_0.10.0 igraph_0.7.1
parallel_3.1.2 rgl_0.95.1201 stats4_3.1.2 tools_3.1.2

On 27 March 2015 at 18:47, Kasper Daniel Hansen [email protected]
wrote:

This looks like a bug. However, I have to point out that the two graphs
are not identical - one is undirected, the other is not and the edge
weights are slightly different. I don't know enough about the internals
of
fdp to know if this makes a difference, but it should be easy to test.

Nevertheless I do think it looks like a bug.

Just for the record: which version of Graphviz did you use for the
command
line example?

—
Reply to this email directly or view it on GitHub
<
#4 (comment)

.

-------- January Weiner --------------------------------------

—
Reply to this email directly or view it on GitHub
#4 (comment)
.

[january3]

fdp - graphviz version 2.36.0 (20140111.2315)

On 27 March 2015 at 19:52, Kasper Daniel Hansen [email protected]
wrote:

I meant command-line graphviz;, just do

fdp -V

Kasper

On Fri, Mar 27, 2015 at 2:47 PM, january3 [email protected]
wrote:

Hi Kasper, version 2.8.1

here is my sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods
base

other attached packages:
[1] Rgraphviz_2.8.1 graph_1.42.0 tmod_0.9 pca3d_0.4
myfuncs_1.5 setwidth_1.0-3 colorout_0.9-9

loaded via a namespace (and not attached):
[1] beeswarm_0.1.6 BiocGenerics_0.10.0 igraph_0.7.1
parallel_3.1.2 rgl_0.95.1201 stats4_3.1.2 tools_3.1.2

On 27 March 2015 at 18:47, Kasper Daniel Hansen <
[email protected]>
wrote:

This looks like a bug. However, I have to point out that the two graphs
are not identical - one is undirected, the other is not and the edge
weights are slightly different. I don't know enough about the internals
of
fdp to know if this makes a difference, but it should be easy to test.

Nevertheless I do think it looks like a bug.

Just for the record: which version of Graphviz did you use for the
command
line example?

—
Reply to this email directly or view it on GitHub
<

#4 (comment)

.

-------- January Weiner --------------------------------------

—
Reply to this email directly or view it on GitHub
<
#4 (comment)

.

—
Reply to this email directly or view it on GitHub
#4 (comment)
.

-------- January Weiner --------------------------------------