Re: [igraph] Node Overlap and Positioning

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Sebastián Goinheix
Instituto de Economía - UdelaR

Tel: 2400 0466 (ext. 2416)

Por favor, evite imprimir este correo.

2017-11-30 9:54 GMT-03:00 Lorenzo Isella <address@hidden>:

Dear All,
I have not used the igraph in a long time, so I am a bit rusty.
Essentially, I would like to make a nice eye-catching plot of a simple network.
Please have a look at

https://ged-project.de/research/studies/factory-europe/

where if you scroll down a bit you find a nice visualization.
I like it because

1) there is no overlapping between the nodes
2) the bigger nodes have a rather central position in the network plot
3) the edges are curved in a very smooth way.

As to 1), from my googling, it appears that igraph has no concept of node size, so you have to fine tune the layout, xlim,ylim and node size yourself. Or has anything changed at this regard?

For 2), what is the recommended layout?

For 3), yes, I can bend the edges, but the result is not nearly as smooth as in that network visualization.
To fix the ideas, please have a look at the self contained example at the end of the email.
Any suggestion is appreciated.
Cheers

Lorenzo

##########################################################

library(igraph)

g <- structure(list(28, FALSE, c(6, 6, 8, 9, 10, 10, 11, 12, 13, 14,
15, 16, 16, 17, 17, 17, 17, 17, 17, 18, 18, 19, 19, 19, 20, 20,
20, 20, 20, 20, 21, 21, 21, 22, 22, 22, 23, 23, 23, 24, 24, 24,
25, 25, 25, 25, 25, 25, 26, 26, 26, 27, 27, 27), c(1, 2, 2, 3,
2, 7, 6, 1, 4, 10, 2, 1, 12, 1, 3, 5, 6, 10, 13, 7, 15, 14, 17,
18, 0, 1, 2, 14, 18, 19, 0, 6, 7, 0, 9, 18, 17, 20, 22, 5, 7,
11, 0, 8, 10, 18, 22, 24, 6, 9, 14, 4, 21, 25), c(0, 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53), c(24, 30, 33, 42, 0, 7, 11, 13, 25, 1, 2, 4, 10, 26, 3,
14, 8, 51, 15, 39, 6, 16, 31, 48, 5, 19, 32, 40, 43, 34, 49,
9, 17, 44, 41, 12, 18, 21, 27, 50, 20, 22, 36, 23, 28, 35, 45,
29, 37, 52, 38, 46, 47, 53), c(0, 0, 0, 0, 0, 0, 0, 2, 2, 3,
4, 6, 7, 8, 9, 10, 11, 13, 19, 21, 24, 30, 33, 36, 39, 42, 48,
51, 54), c(0, 4, 9, 14, 16, 18, 20, 24, 28, 29, 31, 34, 35, 36,
37, 40, 41, 41, 43, 47, 48, 49, 50, 52, 52, 53, 54, 54, 54),
    list(c(1, 0, 1), structure(list(name = "Erdos renyi (gnp) graph",
        type = "gnp", loops = FALSE, p = 0.142857142857143), .Names = c("name",
    "type", "loops", "p")), structure(list(names = c("BE", "BG",
    "CZ", "DK", "DE", "EE", "IE", "EL", "ES", "FR", "IT", "CY",
    "LV", "LT", "LU", "HU", "MT", "NL", "AT", "PL", "PT", "RO",
    "SI", "SK", "FI", "SE", "UK", "HR")), .Names = "names"),
        structure(list(weight = c(16.3104184714332, 30.7293642773093,
        1.51651715633125, 46.5498389394643, 117.400128622748,
        9116.96298628885, 1101.62292417749, 12.3449820775232,
        158.642126867059, 1.81516408646891, 760.982895191571,
        1011.05564809154, 31677.1638228568, 189.344972592696,
        13.1424122833109, 66.5517926330624, 12.0922729908787,
        4.58139821481045, 90.1042955878783, 3.71064650396136,
        90.4281997569113, 158.365362288124, 46.6972207187443,
        30.3317841283049, 7.78960961626955, 1.95560245248322,
        697.72330148994, 58.3866681241721, 660.780592399842,
        1.30621866244087, 90.6566452600129, 411.372413931909,
        50.4594917412583, 30.747955195432, 5.22931377396076,
        26225.4597289607, 518.792688616195, 12998.9635603034,
        69.4202716300456, 8.21344218621299, 0.582827301648975,
        8.09867531337074, 107.652085596974, 1142.61073604216,
        116.541846414264, 1.62280326041373, 405.914678311703,
        0.386623934247936, 18.218603738158, 21.1501080346551,
        0.158066706508139, 862.791072359265, 8.42653129127126,
        20.0432021225717)), .Names = "weight"))), class = "igraph")

g <- upgrade_graph(g)

## l <- layout.fruchterman.reingold(g)

l <- layout_with_dh(g)

l <- layout.norm(l, -1,1, -1,1)

l <- norm_coords(layout.graphopt(g), xmin=-2, xmax=2, ymin=-2, ymax=2)

set.seed(1234)
pdf("toy-network.pdf")

plot(g, layout=l,
     ## rescale=F, ylim=c(0.4,2.6), xlim=c(-3.4, -1.7),
     ## vertex.label.dist=0.5,
     vertex.color=adjustcolor("blue", .5),
     vertex.frame.color="#ff000033",
     edge.color="#55555533",
     vertex.label=V(g)$names,
     vertex.label.color="black",
     vertex.size=log(strength(g))*2,
     edge.width= log(1+E(g)$weight)
    , edge.curved=0.3,
     edge.label=NA    )

dev.off()

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From:	Sebastián Goinheix
Subject:	Re: [igraph] Node Overlap and Positioning
Date:	Thu, 30 Nov 2017 10:33:04 -0300