how to create concentric layout for bipartite graph
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I have a bipartite graph like this where I want one attribute on the outer circle and other attribute either on the inner circle or simply within the outer circle.
According to this question Bioconductor can do something like that, but I don't know how customisable are the fonts etc. Any other methods to create concentric layout for bipartite graph?
r layout graph igraph bioconductor
edited Nov 20 at 4:52
alistaire
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
add a comment |
up vote
1
down vote
favorite
I have a bipartite graph like this where I want one attribute on the outer circle and other attribute either on the inner circle or simply within the outer circle.
According to this question Bioconductor can do something like that, but I don't know how customisable are the fonts etc. Any other methods to create concentric layout for bipartite graph?
r layout graph igraph bioconductor
edited Nov 20 at 4:52
alistaire
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
add a comment |
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I have a bipartite graph like this where I want one attribute on the outer circle and other attribute either on the inner circle or simply within the outer circle.
According to this question Bioconductor can do something like that, but I don't know how customisable are the fonts etc. Any other methods to create concentric layout for bipartite graph?
r layout graph igraph bioconductor
edited Nov 20 at 4:52
alistaire
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
I have a bipartite graph like this where I want one attribute on the outer circle and other attribute either on the inner circle or simply within the outer circle.
According to this question Bioconductor can do something like that, but I don't know how customisable are the fonts etc. Any other methods to create concentric layout for bipartite graph?
r layout graph igraph bioconductor
r layout graph igraph bioconductor
edited Nov 20 at 4:52
alistaire
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
edited Nov 20 at 4:52
alistaire
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
edited Nov 20 at 4:52
alistaire
31.3k43563
edited Nov 20 at 4:52
alistaire
31.3k43563
edited Nov 20 at 4:52
alistaire
31.3k43563
31.3k43563
asked Nov 20 at 4:36
santoku
96711529
asked Nov 20 at 4:36
santoku
96711529
asked Nov 20 at 4:36
santoku
96711529
96711529
add a comment |
add a comment |
1 Answer
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igraph has a bipartite layout that tries to minimize edge crossings. You could run this layout, extract the coordinates, then wrap them around a circle.
I am not experienced enough with R to be able to afford the time to show you how this is done with the R interface. But I can show you what it would look like when you're done, using the Mathematica interface of igraph.
<< IGraphM`
IGraph/M 0.3.103 (November 13, 2018)
Evaluate IGDocumentation to get started.
Generate a sparse random bipartite graph, take its largest connected component, and run the layout. If the graph is not sparse, it won't be possible to avoid edges passing through the middle of the circle.
IGSeedRandom[4];
bg = IGGiantComponent@IGBipartiteGameGNM[100, 100, 220];
bg = IGLayoutBipartite[bg, "BipartitePartitions" -> IGBipartitePartitions[bg]]
Extract the coordinates, and wrap them around two circles.
pts = GraphEmbedding[bg]; (* get vertex coordinates *)
{m1, m2} = Max /@ Values@GroupBy[pts, First -> Last]; (* find max coordinate for both vertex groups *)
newPts = If[#1 == -1,
2 {Cos[#2/m1 2 Pi], Sin[#2/m1 2 Pi]},
3 {Cos[#2/m2 2 Pi], Sin[#2/m2 2 Pi]}
] & @@@ pts; (* wrap both groups around a circle *)
Graph[VertexList[bg], EdgeList[bg], VertexCoordinates -> newPts]
The above uses a circle radius ratio of 3:2. The bigger the radius ratio, the fewer edges cross the inner circle. Here's a plot with a ratio of 3:1.
answered Nov 20 at 16:13
Szabolcs
16k361143
add a comment |
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1 Answer
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1 Answer
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active
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active
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igraph has a bipartite layout that tries to minimize edge crossings. You could run this layout, extract the coordinates, then wrap them around a circle.
I am not experienced enough with R to be able to afford the time to show you how this is done with the R interface. But I can show you what it would look like when you're done, using the Mathematica interface of igraph.
<< IGraphM`
IGraph/M 0.3.103 (November 13, 2018)
Evaluate IGDocumentation to get started.
Generate a sparse random bipartite graph, take its largest connected component, and run the layout. If the graph is not sparse, it won't be possible to avoid edges passing through the middle of the circle.
IGSeedRandom[4];
bg = IGGiantComponent@IGBipartiteGameGNM[100, 100, 220];
bg = IGLayoutBipartite[bg, "BipartitePartitions" -> IGBipartitePartitions[bg]]
Extract the coordinates, and wrap them around two circles.
pts = GraphEmbedding[bg]; (* get vertex coordinates *)
{m1, m2} = Max /@ Values@GroupBy[pts, First -> Last]; (* find max coordinate for both vertex groups *)
newPts = If[#1 == -1,
2 {Cos[#2/m1 2 Pi], Sin[#2/m1 2 Pi]},
3 {Cos[#2/m2 2 Pi], Sin[#2/m2 2 Pi]}
] & @@@ pts; (* wrap both groups around a circle *)
Graph[VertexList[bg], EdgeList[bg], VertexCoordinates -> newPts]
The above uses a circle radius ratio of 3:2. The bigger the radius ratio, the fewer edges cross the inner circle. Here's a plot with a ratio of 3:1.
answered Nov 20 at 16:13
Szabolcs
16k361143
add a comment |
up vote
0
down vote
igraph has a bipartite layout that tries to minimize edge crossings. You could run this layout, extract the coordinates, then wrap them around a circle.
I am not experienced enough with R to be able to afford the time to show you how this is done with the R interface. But I can show you what it would look like when you're done, using the Mathematica interface of igraph.
<< IGraphM`
IGraph/M 0.3.103 (November 13, 2018)
Evaluate IGDocumentation to get started.
Generate a sparse random bipartite graph, take its largest connected component, and run the layout. If the graph is not sparse, it won't be possible to avoid edges passing through the middle of the circle.
IGSeedRandom[4];
bg = IGGiantComponent@IGBipartiteGameGNM[100, 100, 220];
bg = IGLayoutBipartite[bg, "BipartitePartitions" -> IGBipartitePartitions[bg]]
Extract the coordinates, and wrap them around two circles.
pts = GraphEmbedding[bg]; (* get vertex coordinates *)
{m1, m2} = Max /@ Values@GroupBy[pts, First -> Last]; (* find max coordinate for both vertex groups *)
newPts = If[#1 == -1,
2 {Cos[#2/m1 2 Pi], Sin[#2/m1 2 Pi]},
3 {Cos[#2/m2 2 Pi], Sin[#2/m2 2 Pi]}
] & @@@ pts; (* wrap both groups around a circle *)
Graph[VertexList[bg], EdgeList[bg], VertexCoordinates -> newPts]
The above uses a circle radius ratio of 3:2. The bigger the radius ratio, the fewer edges cross the inner circle. Here's a plot with a ratio of 3:1.
answered Nov 20 at 16:13
Szabolcs
16k361143
add a comment |
up vote
0
down vote
up vote
0
down vote
igraph has a bipartite layout that tries to minimize edge crossings. You could run this layout, extract the coordinates, then wrap them around a circle.
I am not experienced enough with R to be able to afford the time to show you how this is done with the R interface. But I can show you what it would look like when you're done, using the Mathematica interface of igraph.
<< IGraphM`
IGraph/M 0.3.103 (November 13, 2018)
Evaluate IGDocumentation to get started.
Generate a sparse random bipartite graph, take its largest connected component, and run the layout. If the graph is not sparse, it won't be possible to avoid edges passing through the middle of the circle.
IGSeedRandom[4];
bg = IGGiantComponent@IGBipartiteGameGNM[100, 100, 220];
bg = IGLayoutBipartite[bg, "BipartitePartitions" -> IGBipartitePartitions[bg]]
Extract the coordinates, and wrap them around two circles.
pts = GraphEmbedding[bg]; (* get vertex coordinates *)
{m1, m2} = Max /@ Values@GroupBy[pts, First -> Last]; (* find max coordinate for both vertex groups *)
newPts = If[#1 == -1,
2 {Cos[#2/m1 2 Pi], Sin[#2/m1 2 Pi]},
3 {Cos[#2/m2 2 Pi], Sin[#2/m2 2 Pi]}
] & @@@ pts; (* wrap both groups around a circle *)
Graph[VertexList[bg], EdgeList[bg], VertexCoordinates -> newPts]
The above uses a circle radius ratio of 3:2. The bigger the radius ratio, the fewer edges cross the inner circle. Here's a plot with a ratio of 3:1.
answered Nov 20 at 16:13
Szabolcs
16k361143
igraph has a bipartite layout that tries to minimize edge crossings. You could run this layout, extract the coordinates, then wrap them around a circle.
I am not experienced enough with R to be able to afford the time to show you how this is done with the R interface. But I can show you what it would look like when you're done, using the Mathematica interface of igraph.
<< IGraphM`
IGraph/M 0.3.103 (November 13, 2018)
Evaluate IGDocumentation to get started.
Generate a sparse random bipartite graph, take its largest connected component, and run the layout. If the graph is not sparse, it won't be possible to avoid edges passing through the middle of the circle.
IGSeedRandom[4];
bg = IGGiantComponent@IGBipartiteGameGNM[100, 100, 220];
bg = IGLayoutBipartite[bg, "BipartitePartitions" -> IGBipartitePartitions[bg]]
Extract the coordinates, and wrap them around two circles.
pts = GraphEmbedding[bg]; (* get vertex coordinates *)
{m1, m2} = Max /@ Values@GroupBy[pts, First -> Last]; (* find max coordinate for both vertex groups *)
newPts = If[#1 == -1,
2 {Cos[#2/m1 2 Pi], Sin[#2/m1 2 Pi]},
3 {Cos[#2/m2 2 Pi], Sin[#2/m2 2 Pi]}
] & @@@ pts; (* wrap both groups around a circle *)
Graph[VertexList[bg], EdgeList[bg], VertexCoordinates -> newPts]
The above uses a circle radius ratio of 3:2. The bigger the radius ratio, the fewer edges cross the inner circle. Here's a plot with a ratio of 3:1.
answered Nov 20 at 16:13
Szabolcs
16k361143
edited Nov 20 at 16:19
answered Nov 20 at 16:13
Szabolcs
16k361143
answered Nov 20 at 16:13
Szabolcs
16k361143
answered Nov 20 at 16:13
Szabolcs
16k361143
16k361143
add a comment |
add a comment |
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