{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/gneiss/issues/4","repository_url":"https://api.github.com/repos/biocore/gneiss","labels_url":"https://api.github.com/repos/biocore/gneiss/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/biocore/gneiss/issues/4/comments","events_url":"https://api.github.com/repos/biocore/gneiss/issues/4/events","html_url":"https://github.com/biocore/gneiss/pull/4","id":163733281,"number":4,"title":"WIP: Adding in balance plot","user":{"login":"mortonjt","id":4184797,"avatar_url":"https://avatars.githubusercontent.com/u/4184797?v=3","gravatar_id":"","url":"https://api.github.com/users/mortonjt","html_url":"https://github.com/mortonjt","followers_url":"https://api.github.com/users/mortonjt/followers","following_url":"https://api.github.com/users/mortonjt/following{/other_user}","gists_url":"https://api.github.com/users/mortonjt/gists{/gist_id}","starred_url":"https://api.github.com/users/mortonjt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mortonjt/subscriptions","organizations_url":"https://api.github.com/users/mortonjt/orgs","repos_url":"https://api.github.com/users/mortonjt/repos","events_url":"https://api.github.com/users/mortonjt/events{/privacy}","received_events_url":"https://api.github.com/users/mortonjt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-04T19:12:34Z","updated_at":"2016-07-05T18:32:29Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biocore/gneiss/pulls/4","html_url":"https://github.com/biocore/gneiss/pull/4","diff_url":"https://github.com/biocore/gneiss/pull/4.diff","patch_url":"https://github.com/biocore/gneiss/pull/4.patch"},"body":"There is the skeleton for the balance plot - this is just used for plotting values on the internal nodes. \r\n\r\nThere are few things that I would like some input for \r\n\r\n1. Testing - the only way that I know how to test this code is using IPython notebooks.  This is because the actual ETE visualizations aren't tested.  But IPython notebooks aren't ideal to review / modify, due to the underlying json.  Another option is to use [ipymd](https://media.readthedocs.org/pdf/ipymd/latest/ipymd.pdf) to render as markdown.  Or we can use Sphinx to display plots.  I'm not sure what the best way forward on this is\r\n2. The balances parameter in `balanceplot` right now only accepts a `np.array` as input, and assumes level ordering.  I think this is good enough for the first pass.  Eventually I'd like to pass in a `pd.Series` to make this easier to use.  The problem with this is the internal nodes within the tree aren't labeled most of the time.\r\n3. Display layouts.  All of the ETE display parameters are enforced within a `layout` function.  I think the default layouts that I have atm are good enough for the first pass, but I'd like to hear some ideas on how to improve the usability of this."},"comment":{"url":"https://api.github.com/repos/biocore/gneiss/issues/comments/230563080","html_url":"https://github.com/biocore/gneiss/pull/4#issuecomment-230563080","issue_url":"https://api.github.com/repos/biocore/gneiss/issues/4","id":230563080,"user":{"login":"antgonza","id":2014559,"avatar_url":"https://avatars.githubusercontent.com/u/2014559?v=3","gravatar_id":"","url":"https://api.github.com/users/antgonza","html_url":"https://github.com/antgonza","followers_url":"https://api.github.com/users/antgonza/followers","following_url":"https://api.github.com/users/antgonza/following{/other_user}","gists_url":"https://api.github.com/users/antgonza/gists{/gist_id}","starred_url":"https://api.github.com/users/antgonza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antgonza/subscriptions","organizations_url":"https://api.github.com/users/antgonza/orgs","repos_url":"https://api.github.com/users/antgonza/repos","events_url":"https://api.github.com/users/antgonza/events{/privacy}","received_events_url":"https://api.github.com/users/antgonza/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T18:32:29Z","updated_at":"2016-07-05T18:32:29Z","body":"I think you can test using [ete's get_ascii]( http://etetoolkit.org/docs/latest/reference/reference_tree.html#ete3.TreeNode.get_ascii), have you tried? \r\n\r\nBTW ipython notebooks render correctly and you can comment on review, for example: [Platypus](https://github.com/biocore/Platypus-Conquistador/blob/master/ipynbs/Chasing_Platypus_via_MG-RAST.ipynb)"}}
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