Entering edit mode
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:
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.