{"action":"created","issue":{"url":"https://api.github.com/repos/leekgroup/recount/issues/9","repository_url":"https://api.github.com/repos/leekgroup/recount","labels_url":"https://api.github.com/repos/leekgroup/recount/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/leekgroup/recount/issues/9/comments","events_url":"https://api.github.com/repos/leekgroup/recount/issues/9/events","html_url":"https://github.com/leekgroup/recount/issues/9","id":216163607,"number":9,"title":"Plot base level coverage","user":{"login":"lcolladotor","id":2288213,"avatar_url":"https://avatars2.githubusercontent.com/u/2288213?v=4","gravatar_id":"","url":"https://api.github.com/users/lcolladotor","html_url":"https://github.com/lcolladotor","followers_url":"https://api.github.com/users/lcolladotor/followers","following_url":"https://api.github.com/users/lcolladotor/following{/other_user}","gists_url":"https://api.github.com/users/lcolladotor/gists{/gist_id}","starred_url":"https://api.github.com/users/lcolladotor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lcolladotor/subscriptions","organizations_url":"https://api.github.com/users/lcolladotor/orgs","repos_url":"https://api.github.com/users/lcolladotor/repos","events_url":"https://api.github.com/users/lcolladotor/events{/privacy}","received_events_url":"https://api.github.com/users/lcolladotor/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2017-03-22T18:20:46Z","updated_at":"2017-07-18T02:14:46Z","closed_at":"2017-07-18T02:14:46Z","body":"I've received feedback from users interested in being able to plot the base-level coverage for a set of samples in [recount2](https://jhubiostatistics.shinyapps.io/recount/).\r\n\r\nOne way of doing this is via `derfinderPlot::plotRegionCoverage()`. I could write a function where the user specifies:\r\n\r\n* (1) a list of sample ids (`run` for SRA and GTEx, `gdc_file_id` for TCGA),\r\n* (2) a GRanges with the regions of interest (which would have to be short -- or the user would be warned) and\r\n* (3) colors and labels for each sample (ideally representing different groups).\r\n\r\nThen internally run `derfinder::loadCoverage()` accessing the data from either local bigwigs (if at JHPCE, SciServer or if the user downloaded them) or via the web. Something that could be a bit of a bottle neck is the annotation needed for `derfinderPlot::plotRegionCoverage()`. That would normally involve creating a genomic state object from Gencode v25 hg38 which takes time even for one chromosome. I could pre-make them split by chr and have the function download the files from the web behind the scenes. In any case, right now this approach would have to deal with\r\n https://github.com/rafalab/bumphunter/issues/15 since `derfinderPlot::plotRegionCoverage()` requires the output of `bumphunter::matchGenes()`. \r\n\r\nAnother option would be to open the data in the UCSC genome browser or something like that. \r\n\r\nA third option could be to use `epivizr` http://bioconductor.org/packages/release/bioc/vignettes/epivizr/inst/doc/IntroToEpivizr.html. Although I'm not sure that it can read bigwig files from the web.\r\n\r\nThoughts @andrewejaffe @jtleek ?\r\n\r\nRight now, users can get the list of URLs from `recount::recount_url` and load them into IGV or similar programs.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/leekgroup/recount/issues/comments/315938325","html_url":"https://github.com/leekgroup/recount/issues/9#issuecomment-315938325","issue_url":"https://api.github.com/repos/leekgroup/recount/issues/9","id":315938325,"user":{"login":"lcolladotor","id":2288213,"avatar_url":"https://avatars2.githubusercontent.com/u/2288213?v=4","gravatar_id":"","url":"https://api.github.com/users/lcolladotor","html_url":"https://github.com/lcolladotor","followers_url":"https://api.github.com/users/lcolladotor/followers","following_url":"https://api.github.com/users/lcolladotor/following{/other_user}","gists_url":"https://api.github.com/users/lcolladotor/gists{/gist_id}","starred_url":"https://api.github.com/users/lcolladotor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lcolladotor/subscriptions","organizations_url":"https://api.github.com/users/lcolladotor/orgs","repos_url":"https://api.github.com/users/lcolladotor/repos","events_url":"https://api.github.com/users/lcolladotor/events{/privacy}","received_events_url":"https://api.github.com/users/lcolladotor/received_events","type":"User","site_admin":false},"created_at":"2017-07-18T02:14:46Z","updated_at":"2017-07-18T02:14:46Z","body":"The tutorial using `derfinderPlot` is part of https://github.com/LieberInstitute/recountWorkflow. I mentioned wiggleplotr and epivizR as other options.  Showing how to use all the different tools could be a workflow itself, but for now that is out of the scope of the recount workflow I wrote. In any case, the workflow addresses this issue, so I'll close it for now."}}
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