{"action":"created","issue":{"url":"https://api.github.com/repos/RCollins13/CNView/issues/1","repository_url":"https://api.github.com/repos/RCollins13/CNView","labels_url":"https://api.github.com/repos/RCollins13/CNView/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/RCollins13/CNView/issues/1/comments","events_url":"https://api.github.com/repos/RCollins13/CNView/issues/1/events","html_url":"https://github.com/RCollins13/CNView/issues/1","id":149498898,"number":1,"title":"Plotting samples to example.pdf...Error in x[j] : invalid subscript type 'list'","user":{"login":"raymond301","id":392344,"avatar_url":"https://avatars.githubusercontent.com/u/392344?v=3","gravatar_id":"","url":"https://api.github.com/users/raymond301","html_url":"https://github.com/raymond301","followers_url":"https://api.github.com/users/raymond301/followers","following_url":"https://api.github.com/users/raymond301/following{/other_user}","gists_url":"https://api.github.com/users/raymond301/gists{/gist_id}","starred_url":"https://api.github.com/users/raymond301/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/raymond301/subscriptions","organizations_url":"https://api.github.com/users/raymond301/orgs","repos_url":"https://api.github.com/users/raymond301/repos","events_url":"https://api.github.com/users/raymond301/events{/privacy}","received_events_url":"https://api.github.com/users/raymond301/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-19T15:38:19Z","updated_at":"2016-04-19T15:58:29Z","closed_at":null,"body":"Have an input file with coverage from 30 samples, across 1 gene.\r\nEach row in the bed file covers 100bp, like shown in your example.\r\nHere is my command: \r\n```\r\n/data2/bsi/staff_analysis/m088378/CNView.R 17 41205689 41277589 PDXsamples.names.txt PDXsamples.chrless.bed example.pdf --probs\r\n```\r\nI am following the format exactly specified. However I get this error:\r\n\r\n```\r\n+-------------------+\r\n| CNView Visualizer |\r\n|     (c) 2016      |\r\n+-------------------+\r\nReading sample IDs from PDXsamples.names.txt\r\nFiltering & loading coverage matrix... Complete\r\nCompressing coverage matrix [900 bp bins]...  Complete\r\nPerforming intra-sample normalization... Complete\r\nPerforming inter-sample normalization... Complete\r\nPlotting samples to example.pdf...Error in x[j] : invalid subscript type 'list'\r\nCalls: CNView -> pt -> [ -> [.data.frame\r\nExecution halted\r\n```\r\n\r\nI'm going to start going through the code step by step, but I thought I'd create an issue to make you aware of a potential situation that the code is not handling."},"comment":{"url":"https://api.github.com/repos/RCollins13/CNView/issues/comments/211993563","html_url":"https://github.com/RCollins13/CNView/issues/1#issuecomment-211993563","issue_url":"https://api.github.com/repos/RCollins13/CNView/issues/1","id":211993563,"user":{"login":"raymond301","id":392344,"avatar_url":"https://avatars.githubusercontent.com/u/392344?v=3","gravatar_id":"","url":"https://api.github.com/users/raymond301","html_url":"https://github.com/raymond301","followers_url":"https://api.github.com/users/raymond301/followers","following_url":"https://api.github.com/users/raymond301/following{/other_user}","gists_url":"https://api.github.com/users/raymond301/gists{/gist_id}","starred_url":"https://api.github.com/users/raymond301/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/raymond301/subscriptions","organizations_url":"https://api.github.com/users/raymond301/orgs","repos_url":"https://api.github.com/users/raymond301/repos","events_url":"https://api.github.com/users/raymond301/events{/privacy}","received_events_url":"https://api.github.com/users/raymond301/received_events","type":"User","site_admin":false},"created_at":"2016-04-19T15:58:29Z","updated_at":"2016-04-19T15:58:29Z","body":"As I was digging into the code, I did discover a different issue. Semi-unrelated.\r\n\r\nLine 206:\r\n```R\r\n##Generate Colors##\r\n      if(pt(plotSet[1,sampIdx[k]],df=(ncol(plotSet)-8)) >= 1-(0.05/(ncol(plotSet)-7))){\r\n        colval <- \"blue\"\r\n      }else if(pt(plotSet[1,sampIdx[k]],df=(ncol(plotSet)-8)) <= 0.05/(ncol(plotSet)-7)){\r\n        colval <- \"red\"\r\n      }else{\r\n        colval <- \"gray40\"\r\n      }\r\n```\r\n\r\nThe 1st sample name I provided was \"sample3-1\", which caused\r\n```R\r\nsampIdx[k] = integer(0)\r\n```\r\n\r\nI'm still working on the original issue, but error handling names with hyphens would be a nice addition. I'll just avoid it for this version."}}