overlap using circo

HI,
 
I am trying to use circo to plot my graph but the nodes are overlapping?!?!
 
What should I do?
 
thanks,
anna

AttachmentSize
GENES_REFSEQ_14_circo_WATERFALL.png31.48 KB

overlap using circo

I'm a bit surprised at that output. circo does take node sizes into account, and shouldn't produce that much overlap. Would you post the original graph please? Thanks.
To answer your question, use the overlap attribute to remove overlaps. Using overlap=scale uniformly scales up the drawing. This preserves the shape of the graph, but can use a lot of area. If available, overlap=prism will try to keep the rough shape of the layout but use a lot less area.

overlap using circo...

Thanks for answering, the graph is below:
 
strict digraph {
    graph [bb="0,0,477.78,100",
        bgcolor=white,
        overlap=prism
    ];
    node [label="\N"];
    EIF3C     [color=red,
        height="0.5",
        pos="231.19,74",
        width="1.0055"];
    EIF3C -> EIF3C     [color=white,
        pos="e,265.19,67.25 265.19,80.75 276.52,80.75 285.58,78.5 285.58,74 285.58,70.977 281.49,68.969 275.37,67.977"];
    HIST2H2AA4     [color=red,
        height="0.5",
        pos="206.89,50",
        width="1.8374"];
    HIST2H2AA3     [color=black,
        height="0.5",
        pos="411.48,50",
        width="1.8374"];
    HIST2H2AA4 -> HIST2H2AA3     [color=black,
        pos="e,345.04,50 273.32,50 292.98,50 314.67,50 334.92,50"];
    EIF3CL     [color=red,
        height="0.5",
        pos="175.19,18",
        width="1.1701"];
    EIF3CL -> EIF3CL     [color=white,
        pos="e,214.59,11.265 214.59,24.735 226.31,24.534 235.43,22.289 235.43,18 235.43,15.051 231.12,13.069 224.62,12.052"];
    TMEM106C     [color=red,
        height="0.5",
        pos="191.19,82",
        width="1.6499"];
    TMEM106C -> TMEM106C     [color=white,
        pos="e,247.13,75.415 247.13,88.585 259.75,87.992 268.98,85.797 268.98,82 268.98,79.33 264.42,77.453 257.32,76.367"];
    MIER1     [color=red,
        height="0.5",
        pos="38.997,38",
        width="1.0694"];
    MIER1 -> MIER1     [color=black,
        pos="e,75.174,31.252 75.174,44.748 86.788,44.679 95.993,42.43 95.993,38 95.993,35.024 91.838,33.032 85.589,32.024"];
    EMR2     [color=black,
        height="0.5",
        pos="186.39,38",
        width="1.0055"];
    MIER1 -> EMR2     [color=white,
        pos="e,149.88,38 78.108,38 97.064,38 119.97,38 139.82,38"];
    HSPA1A     [color=red,
        height="0.5",
        pos="187.04,62",
        width="1.2888"];
    HSPA1B     [color=black,
        height="0.5",
        pos="351.98,62",
        width="1.2798"];
    HSPA1A -> HSPA1B     [color=white,
        pos="e,305.61,62 233.87,62 253.01,62 275.32,62 295.37,62"];
    F8A1     [color=red,
        height="0.5",
        pos="203.19,26",
        width="0.89579"];
    F8A1 -> F8A1     [color=black,
        pos="e,233.51,19.26 233.51,32.74 244.6,32.922 253.69,30.676 253.69,26 253.69,22.858 249.58,20.814 243.53,19.865"];
    C8ORF30A     [color=red,
        height="0.5",
        pos="223.19,26",
        width="1.586"];
    C8ORF30A -> C8ORF30A     [color=white,
        pos="e,276.58,19.383 276.58,32.617 289.13,32.073 298.38,29.867 298.38,26 298.38,23.281 293.81,21.383 286.73,20.307"];
    NM_172358     [color=red,
        height="0.5",
        pos="354.58,38",
        width="1.6499"];
    NM_172358 -> EMR2     [color=white,
        pos="e,222.76,38 294.34,38 274.13,38 251.93,38 232.94,38"];
    percent     [color=black,
        fontsize=14,
        height="0.5",
        label=14,
        pos="211.19,74",
        width="0.75"];
}
 

overlap using circo...

This is a bug introduced into circo in 2.28. It has now been fixed. Tomorrow's packages will contain the patch.

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