{"action":"created","issue":{"url":"https://api.github.com/repos/stephenturner/qqman/issues/23","labels_url":"https://api.github.com/repos/stephenturner/qqman/issues/23/labels{/name}","comments_url":"https://api.github.com/repos/stephenturner/qqman/issues/23/comments","events_url":"https://api.github.com/repos/stephenturner/qqman/issues/23/events","html_url":"https://github.com/stephenturner/qqman/issues/23","id":59537371,"number":23,"title":"Lines","user":{"login":"bthada","id":11278177,"avatar_url":"https://avatars.githubusercontent.com/u/11278177?v=3","gravatar_id":"","url":"https://api.github.com/users/bthada","html_url":"https://github.com/bthada","followers_url":"https://api.github.com/users/bthada/followers","following_url":"https://api.github.com/users/bthada/following{/other_user}","gists_url":"https://api.github.com/users/bthada/gists{/gist_id}","starred_url":"https://api.github.com/users/bthada/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bthada/subscriptions","organizations_url":"https://api.github.com/users/bthada/orgs","repos_url":"https://api.github.com/users/bthada/repos","events_url":"https://api.github.com/users/bthada/events{/privacy}","received_events_url":"https://api.github.com/users/bthada/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-02T19:49:17Z","updated_at":"2015-03-03T20:44:08Z","closed_at":"2015-03-02T21:44:14Z","body":"Stephen, qqman has been great help in making Manhattan plots of my results. I would like to add vertical lines for things like candidate genes and horizontal lines for a comparison with a QTL analysis. Currently I am able to do it when using a subset of just one chromosome but it gives me \"Error: unexpected input...\" when trying to use it for the whole genome wide analysis. Any help would be much appreciated. My current code for the single chromosome is:\r\n\r\nmanhattan(subset(ratioresults, CHR==1), highlight=snpsofinterest)\r\nlines(c(122,145),c(6,6),col=\"green\",lwd=2)\r\nlines(c(32.9,56.62),c(6,6),col=\"green\",lwd=2)\r\nabline(v=50,col=\"green\")\r\n\r\nAn image of the single chromosome and they types of lines I am talking about:\r\n\r\n![image](https://cloud.githubusercontent.com/assets/11278177/6448848/bc8ef0d2-c0ea-11e4-8aa6-ee79d5881eee.png)\r\n\r\nThanks,\r\nBrad"},"comment":{"url":"https://api.github.com/repos/stephenturner/qqman/issues/comments/77030452","html_url":"https://github.com/stephenturner/qqman/issues/23#issuecomment-77030452","issue_url":"https://api.github.com/repos/stephenturner/qqman/issues/23","id":77030452,"user":{"login":"bthada","id":11278177,"avatar_url":"https://avatars.githubusercontent.com/u/11278177?v=3","gravatar_id":"","url":"https://api.github.com/users/bthada","html_url":"https://github.com/bthada","followers_url":"https://api.github.com/users/bthada/followers","following_url":"https://api.github.com/users/bthada/following{/other_user}","gists_url":"https://api.github.com/users/bthada/gists{/gist_id}","starred_url":"https://api.github.com/users/bthada/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bthada/subscriptions","organizations_url":"https://api.github.com/users/bthada/orgs","repos_url":"https://api.github.com/users/bthada/repos","events_url":"https://api.github.com/users/bthada/events{/privacy}","received_events_url":"https://api.github.com/users/bthada/received_events","type":"User","site_admin":false},"created_at":"2015-03-03T20:44:08Z","updated_at":"2015-03-03T20:44:08Z","body":"Stephen,\n\nThat ended up working for me. For some reason, numbers I used when looking\nat the single chromosome where taken as Mb, but for the whole genome it was\nin bp. The numbers I was using were too small to the point of not showing\nup on the graph. Once I switched my code to numbers 1,000,000x those I used\nbefore, it worked just fine when looking at the whole genome. Once I ran\nyour code, I was able to see that. Thanks for the help.\n\nBrad Thada\n\nGraduate Research Assistant\nPurdue University\nAgronomy Department\nPlant Breeding and Genetics\nhttps://ag.purdue.edu/agry/directory/Pages/bthada.aspx\n\nOn Mon, Mar 2, 2015 at 4:44 PM, Stephen Turner <notifications@github.com>\nwrote:\n\n> Closed #23 <https://github.com/stephenturner/qqman/issues/23>.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/stephenturner/qqman/issues/23#event-244755152>.\n>\n"}}