{"action":"created","issue":{"url":"https://api.github.com/repos/ccagc/QDNAseq/issues/13","labels_url":"https://api.github.com/repos/ccagc/QDNAseq/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/ccagc/QDNAseq/issues/13/comments","events_url":"https://api.github.com/repos/ccagc/QDNAseq/issues/13/events","html_url":"https://github.com/ccagc/QDNAseq/pull/13","id":119012613,"number":13,"title":"Add Mbp numbers to x-axis when plotting a single chromosome","user":{"login":"ilarischeinin","id":2540173,"avatar_url":"https://avatars.githubusercontent.com/u/2540173?v=3","gravatar_id":"","url":"https://api.github.com/users/ilarischeinin","html_url":"https://github.com/ilarischeinin","followers_url":"https://api.github.com/users/ilarischeinin/followers","following_url":"https://api.github.com/users/ilarischeinin/following{/other_user}","gists_url":"https://api.github.com/users/ilarischeinin/gists{/gist_id}","starred_url":"https://api.github.com/users/ilarischeinin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ilarischeinin/subscriptions","organizations_url":"https://api.github.com/users/ilarischeinin/orgs","repos_url":"https://api.github.com/users/ilarischeinin/repos","events_url":"https://api.github.com/users/ilarischeinin/events{/privacy}","received_events_url":"https://api.github.com/users/ilarischeinin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-26T10:16:03Z","updated_at":"2015-11-26T13:18:50Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ccagc/QDNAseq/pulls/13","html_url":"https://github.com/ccagc/QDNAseq/pull/13","diff_url":"https://github.com/ccagc/QDNAseq/pull/13.diff","patch_url":"https://github.com/ccagc/QDNAseq/pull/13.patch"},"body":"When plotting a single chromosome (with `plot()` or `frequencyPlot()`), the x-axis used to only display the name of that chromosome (pretty useless). This adds Mbp numbers along the axis.\r\n\r\nThe second commit fixes a bug in plotting `cghRaw/cghSeg/CghCall` objects. QDNAseq plotting can be used for these objects by manually overriding CGHbase's own plotting functions with the commands below. This is handy when one wants to make an array and NGS profile comparable, but is probably used by nobody else.\r\n\r\n```{r}\r\nsetMethod(\"plot\", signature(x=\"cghRaw\", y=\"missing\"),\r\n    getMethod(\"plot\", signature=c(x=\"QDNAseqSignals\", y=\"missing\")))\r\nsetMethod(\"plot\", signature(x=\"cghSeg\", y=\"missing\"),\r\n    getMethod(\"plot\", signature=c(x=\"QDNAseqSignals\", y=\"missing\")))\r\nsetMethod(\"plot\", signature(x=\"cghCall\", y=\"missing\"),\r\n    getMethod(\"plot\", signature=c(x=\"QDNAseqSignals\", y=\"missing\")))\r\nsetMethod(\"frequencyPlot\", signature(x=\"cghCall\", y=\"missing\"),\r\n    getMethod(\"frequencyPlot\",signature=c(x=\"QDNAseqCopyNumbers\", y=\"missing\")))\r\n```\r\n\r\nBy the way, repo `ccagc/QDNAseq` used to contain both `devel` and `develop` branches, which seemed confusing. I merged `devel` to `develop` and deleted it.\r\n\r\nAlso, not really sure what kind of strategy you'd like to use for repos, branches and pull requests. I figured I'd keep my commits to my own fork, and then make pull requests. Also, I made this one to `develop` instead of `master`, so you have control over when things get synced to Bioconductor. Happy to use another strategy if you'd prefer."},"comment":{"url":"https://api.github.com/repos/ccagc/QDNAseq/issues/comments/159909852","html_url":"https://github.com/ccagc/QDNAseq/pull/13#issuecomment-159909852","issue_url":"https://api.github.com/repos/ccagc/QDNAseq/issues/13","id":159909852,"user":{"login":"daoud-sie","id":4175342,"avatar_url":"https://avatars.githubusercontent.com/u/4175342?v=3","gravatar_id":"","url":"https://api.github.com/users/daoud-sie","html_url":"https://github.com/daoud-sie","followers_url":"https://api.github.com/users/daoud-sie/followers","following_url":"https://api.github.com/users/daoud-sie/following{/other_user}","gists_url":"https://api.github.com/users/daoud-sie/gists{/gist_id}","starred_url":"https://api.github.com/users/daoud-sie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daoud-sie/subscriptions","organizations_url":"https://api.github.com/users/daoud-sie/orgs","repos_url":"https://api.github.com/users/daoud-sie/repos","events_url":"https://api.github.com/users/daoud-sie/events{/privacy}","received_events_url":"https://api.github.com/users/daoud-sie/received_events","type":"User","site_admin":false},"created_at":"2015-11-26T13:18:50Z","updated_at":"2015-11-26T13:18:50Z","body":"Thanx Ilari. Looks good.\r\n\r\nLet's adopt [Git-branching-model.pdf](https://github.com/ccagc/QDNAseq/files/44975/Git-branching-model.pdf) from now on, so pushing to develop is the norm for new features. Bug fixes should go to the release branch, and from there merged with the development branch.\r\n\r\nI will push this change to bioconductor svn (dev) once I finish the work on binReadCounts."}}