{"action":"closed","issue":{"url":"https://api.github.com/repos/RGLab/ggcyto/issues/1","labels_url":"https://api.github.com/repos/RGLab/ggcyto/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/RGLab/ggcyto/issues/1/comments","events_url":"https://api.github.com/repos/RGLab/ggcyto/issues/1/events","html_url":"https://github.com/RGLab/ggcyto/issues/1","id":82618926,"number":1,"title":"display the raw scale for transformed data","user":{"login":"mikejiang","id":1385649,"avatar_url":"https://avatars.githubusercontent.com/u/1385649?v=3","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},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-05-29T22:53:25Z","updated_at":"2015-07-17T19:43:57Z","closed_at":"2015-07-17T19:43:57Z","body":"As we've seen during the meeting, to display the transformed data in `raw` scale, we currently do this by customizing the `breaks` and `labels` through `scale_x_continous`.  \r\nMeanwhile we set `limits` to filter out `boundary` event.\r\nBut `limits` within `scale_x_continous` will affect the `geom_gate` layer as well. So we thought about using `coord_trans` instead. e.g.\r\n```r\r\np + coord_trans(xtrans = \"inverse_biexp\", limx = c(0, 4096))\r\n```\r\nEven though, `limits` in `coord_trans` won't affect the data (including `geom_gate`), it does `transform` the data in the end. (I've confirmed it by reading `ggplot` docs and source code).\r\n\r\n> The difference between transforming the scales and transforming the coordinate system is that scale transformation occurs BEFORE statistics, coordinate trans AFTER.\r\n\r\nSo both do the `transformation` to data before the plot is rendered, which is not what we want since data is already transformed.\r\n\r\nBesides, we do want to remove these `outlier events` before the `statistics` calculation (since they mess up the color `fill_gradient` of `hexbin`). So `coord_trans` or `coord_cartesian` won't be the good choice here.\r\n\r\nThe solution would be:\r\n1. still uses `scale_x_continous` to set `breaks` and `labels` for `raw` scales, but without `limits` settings\r\n2. do the `boundary event` filtering somewhere else (e.g. within `fortify` method) and have the option to switch it on/off\r\n\r\n@raphg @gfinak ?\r\n \r\n\r\n"}}