How to convert TreeMix newick output graph to dot format?
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23 months ago
eyb ▴ 250

I ran TreeMix on my populations and got a graph in newick format. I want to use it in GRoSS to find alleles under selective pressure. I've converted newick to dot using newick-to-dot script I found on github, but when I try to run GRoSS I get the following error:

enter image description here

I also tried to read it using ADMIXTOOLS, but I also got the following error:

initgraph = parse_dot(dotfile = "./Newick-To-DOT/YRI_14_treemix_out.dot")
Error in igraph::graph_from_edgelist(.) :                                                                                    
  graph_from_edgelist expects a matrix with two columns

My graph came out horizontal from TreeMix, is this a problem? Can anybody advise? Thanks

graph {
    rankdir=LR;
    splines=line;
    node [shape=none]
    "4fb640" [shape="point"];
    "04fe4d" [shape="point"];
    "4fb640" -- "04fe4d" [shape="point"];
    "2dc477" [label="YRI"];
    "04fe4d" -- "2dc477" ;
    "3a695a" [shape="point"];
    "04fe4d" -- "3a695a" ;
    "8903c6" [shape="point"];
    "3a695a" -- "8903c6" ;
    "15bbe6" [shape="point"];
    "8903c6" -- "15bbe6" ;
    "333740" [shape="point"];
    "15bbe6" -- "333740" ;
    "ac10d6" [label="nenets"];
    "333740" -- "ac10d6" ;
    "360377" [shape="point"];
    "333740" -- "360377" ;
    "c07b3f" [label="CHB"];
    "360377" -- "c07b3f" ;
    "e008f6" [label="yakut"];
    "360377" -- "e008f6" ;
    "d8a2fd" [label="khanty"];
    "15bbe6" -- "d8a2fd" ;
    "da49ed" [label="mansi"];
    "8903c6" -- "da49ed" ;
    "a83fc8" [shape="point"];
    "3a695a" -- "a83fc8" ;
    "28ba57" [label="obiachevo"];
    "a83fc8" -- "28ba57" ;
    "002b2b" [shape="point"];
    "a83fc8" -- "002b2b" ;
    "8c8670" [label="izhma"];
    "002b2b" -- "8c8670" ;
    "1e839d" [shape="point"];
    "002b2b" -- "1e839d" ;
    "0bf962" [label="mezen"];
    "1e839d" -- "0bf962" ;
    "570663" [shape="point"];
    "1e839d" -- "570663" ;
    "8fc8d3" [label="veps"];
    "570663" -- "8fc8d3" ;
    "2824b7" [shape="point"];
    "570663" -- "2824b7" ;
    "8f9748" [label="FIN"];
    "2824b7" -- "8f9748" ;
    "c31951" [shape="point"];
    "2824b7" -- "c31951" ;
    "29dccd" [shape="point"];
    "c31951" -- "29dccd" ;
    "f0cdeb" [label="tver_staritsa"];
    "29dccd" -- "f0cdeb" ;
    "899703" [shape="point"];
    "29dccd" -- "899703" ;
    "c8860d" [label="TSI"];
    "899703" -- "c8860d" ;
    "938755" [label="CEU"];
    "899703" -- "938755" ;
    "4da100" [label="ustujna"];
    "c31951" -- "4da100" ;
}

The graph file.

treemix GRoSS admixtools Newick dot • 561 views
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