{"action":"created","issue":{"url":"https://api.github.com/repos/RGLab/openCyto/issues/158","repository_url":"https://api.github.com/repos/RGLab/openCyto","labels_url":"https://api.github.com/repos/RGLab/openCyto/issues/158/labels{/name}","comments_url":"https://api.github.com/repos/RGLab/openCyto/issues/158/comments","events_url":"https://api.github.com/repos/RGLab/openCyto/issues/158/events","html_url":"https://github.com/RGLab/openCyto/issues/158","id":271061056,"number":158,"title":"Registering flowDensity gating in openCyto does not work.","user":{"login":"BenPVD","id":20134063,"avatar_url":"https://avatars3.githubusercontent.com/u/20134063?v=4","gravatar_id":"","url":"https://api.github.com/users/BenPVD","html_url":"https://github.com/BenPVD","followers_url":"https://api.github.com/users/BenPVD/followers","following_url":"https://api.github.com/users/BenPVD/following{/other_user}","gists_url":"https://api.github.com/users/BenPVD/gists{/gist_id}","starred_url":"https://api.github.com/users/BenPVD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenPVD/subscriptions","organizations_url":"https://api.github.com/users/BenPVD/orgs","repos_url":"https://api.github.com/users/BenPVD/repos","events_url":"https://api.github.com/users/BenPVD/events{/privacy}","received_events_url":"https://api.github.com/users/BenPVD/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-11-03T17:40:51Z","updated_at":"2017-11-03T18:36:17Z","closed_at":null,"author_association":"NONE","body":"Hi everybody,\r\n\r\nI am trying to register gating methods from the flowDensity package to openCyto, but up to this point with no success.\r\n\r\nI have read the threads here regarding registering flowDensity gating to openCyto using the following code:\r\n\r\n`.flowDensity <- function(fr, pp_res, channels=NA, filterId=\"\",...){\r\n    if(length(channels)==2)\r\n    flowDensity:::.flowDensity.2d(fr, channels = channels, ...)\r\n  else\r\n    flowDensity:::.flowDensity.1d(fr, channel = channels, ...)\r\n  }\r\nregisterPlugins(fun = .flowDensity,\r\n                methodName = \"flowDensity\",\r\n                dep = 'flowDensity',\r\n                'gating')`\r\n\r\nThis will create a registered \"flowDensity\" gate when executing the `listgtMethods()` command, but after executing the gating method within my gating template this error comes up:\r\n\r\n`Error in flowDensity:::.flowDensity.2d(fr, channels = channels, ...) : \r\n  object 'remove.margins' not found`\r\n\r\nI checked the flowDensity package and can't find `flowDensity.1d` or `flowDensity.2d`functions within the manual, so I tried to change the wrapper function which was posted here earlier. Again without success.\r\n\r\n`Error in .densityGating(flow.frame = obj, channel, n.sd = n.sd, use.percentile = use.percentile,  : \r\n  formal argument \"flow.frame\" matched by multiple actual arguments`\r\n\r\nCan anyone help?\r\nMaybe simply post the code for registering the `flowDensity` gating to opencyto from the beginning to the end?\r\nAdditionally, I was trying to find the source code from the pre-registered gating functions in order to see how this works there, but commands like `UseMethod()`, `method()` or `stats:::` did not work. Any idea how to get the source code of the pre-registered gating methods of openCyto?\r\n\r\nThanks for your help!"},"comment":{"url":"https://api.github.com/repos/RGLab/openCyto/issues/comments/341791190","html_url":"https://github.com/RGLab/openCyto/issues/158#issuecomment-341791190","issue_url":"https://api.github.com/repos/RGLab/openCyto/issues/158","id":341791190,"user":{"login":"mikejiang","id":1385649,"avatar_url":"https://avatars1.githubusercontent.com/u/1385649?v=4","gravatar_id":"","url":"https://api.github.com/users/mikejiang","html_url":"https://github.com/mikejiang","followers_url":"https://api.github.com/users/mikejiang/followers","following_url":"https://api.github.com/users/mikejiang/following{/other_user}","gists_url":"https://api.github.com/users/mikejiang/gists{/gist_id}","starred_url":"https://api.github.com/users/mikejiang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikejiang/subscriptions","organizations_url":"https://api.github.com/users/mikejiang/orgs","repos_url":"https://api.github.com/users/mikejiang/repos","events_url":"https://api.github.com/users/mikejiang/events{/privacy}","received_events_url":"https://api.github.com/users/mikejiang/received_events","type":"User","site_admin":false},"created_at":"2017-11-03T18:36:17Z","updated_at":"2017-11-03T18:36:17Z","author_association":"OWNER","body":"both `.deGate2D` and `.flowDensity.2d` are private functions defined in `flowDensity` package. You can see the source by adding namespace prefix `flowDensity:::`.\r\nOr view the source from bioc git mirror site\r\nhttps://github.com/Bioconductor-mirror/flowDensity/blob/master/R/helper_functions.R#L118\r\nhttps://github.com/Bioconductor-mirror/flowDensity/blob/master/R/openCyto_wrappers.R#L60\r\n\r\nAs @gfinak said, you should contact its maintainer(Mehrnoush Malek <mmalekes@bccrc.ca>) for the fix (which should be an easy one).\r\n"}}
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