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POspacing vertices evenly in igraph in r
 

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  1. POspacing vertices evenly in igraph in r
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    <p>I have the following graph graph</p> <pre><code>set.seed(1410) df&lt;-data.frame( "site.x"=c(rep("a",3),rep("b",3),rep("c",3),rep("d",3)), "site.y"=c(rep(c("e","f","g"),4)), "bond.strength"=sample(1:100,12, replace=TRUE)) library(igraph) df&lt;-graph.data.frame(df) V(df)$names &lt;- c("a","b","c","d","e","f","g") layOUT&lt;-data.frame(x=c(rep(1,4),rep(2,3)),y=c(4:1,3:1)) E(df)[ bond.strength &lt; 101 ]$color &lt;- "red" E(df)[ bond.strength &lt; 67 ]$color &lt;- "yellow" E(df)[ bond.strength &lt; 34 ]$color &lt;- "green" V(df)$color &lt;- "white" l&lt;-as.matrix(layOUT) plot(df,layout=l,vertex.size=10,vertex.label=V(df)$names, edge.arrow.size=0.01,vertex.label.color = "black") </code></pre> <p><img src="https://i.stack.imgur.com/NWmkh.png" alt="enter image description here"></p> <p>I would like to space the vertices "g-e" evenly along the vertical distance between vertex a and d to make my current graph (see below) prettier. As you can see it is pretty crowded. </p> <p><img src="https://i.stack.imgur.com/7nw2d.png" alt="enter image description here"></p> <p>Also I would like to move the two column of vertices closer together on the x-axis but I have noticed that adjusting the x coordinates in the layout is not responding. For example the two following layouts produce graph that look exactly the same despite the drastic adjustment in the x-coordinates. </p> <pre><code>layOUT&lt;-data.frame(x=c(rep(1,4),rep(2,3)),y=c(4:1,3:1)) layOUT&lt;-data.frame(x=c(rep(1,4),rep(100,3)),y=c(4:1,3:1)) </code></pre> <p>Thanks for any advice you may have.</p>
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    1. USElizabeth
    1. USElizabeth
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      1. VTUpMod
    1. COJust a thought: having this much elements heatmaps might my easier to interpret http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/
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      1. POspacing vertices evenly in igraph in r
      1. USJulius Vainora
    2. COI was thinking about that but I also need to show the size of the vertices as well as their relationship. Can this be done in a heat map?
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      1. POspacing vertices evenly in igraph in r
      1. USElizabeth
    3. COOh, I actually missed the size of the vertices.. well, maybe that would be possible to change the colour of species names instead of size
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      1. POspacing vertices evenly in igraph in r
      1. USJulius Vainora
 

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