{"action":"closed","number":52,"pull_request":{"url":"https://api.github.com/repos/greenelab/multi-plier/pulls/52","id":238979402,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM4OTc5NDAy","html_url":"https://github.com/greenelab/multi-plier/pull/52","diff_url":"https://github.com/greenelab/multi-plier/pull/52.diff","patch_url":"https://github.com/greenelab/multi-plier/pull/52.patch","issue_url":"https://api.github.com/repos/greenelab/multi-plier/issues/52","number":52,"state":"closed","locked":false,"title":"Pathway separation","user":{"login":"jaclyn-taroni","id":19534205,"node_id":"MDQ6VXNlcjE5NTM0MjA1","avatar_url":"https://avatars0.githubusercontent.com/u/19534205?v=4","gravatar_id":"","url":"https://api.github.com/users/jaclyn-taroni","html_url":"https://github.com/jaclyn-taroni","followers_url":"https://api.github.com/users/jaclyn-taroni/followers","following_url":"https://api.github.com/users/jaclyn-taroni/following{/other_user}","gists_url":"https://api.github.com/users/jaclyn-taroni/gists{/gist_id}","starred_url":"https://api.github.com/users/jaclyn-taroni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaclyn-taroni/subscriptions","organizations_url":"https://api.github.com/users/jaclyn-taroni/orgs","repos_url":"https://api.github.com/users/jaclyn-taroni/repos","events_url":"https://api.github.com/users/jaclyn-taroni/events{/privacy}","received_events_url":"https://api.github.com/users/jaclyn-taroni/received_events","type":"User","site_admin":false},"body":"Closes #40 \r\n\r\nHere, I'm adding a notebook (`32-explore_pathway_separation.Rmd`) that looks into the notion of \"pathway separation.\" The logic in `CheckPathwaySeparation` is the part where another set of :eyes: would be most appreciated/helpful!\r\n\r\n----\r\n\r\nI define **pathway separation** to be: Given two sets of related gene sets (a set of related gene sets would be all the monocyte/macrophage gene sets) that are somewhat similar (e.g., neutrophil set and monocyte/macrophage set), does the model: 1) have at least one latent variable significantly associated with at least one pathway in both sets (e.g. both sets are captured)? 2) have each set _uniquely_ or _separately_ represented (e.g., there exists at least one latent variable that is not significantly associated with both sets of and this is true for both sets)?\r\n\r\nTo be a bit more concrete: a model has at least one neutrophil-associated LV that is not associated with any of the monocyte/macrophage gene sets and at least one monocyte/macrophage-associated LV that is not associated with any of the neutrophil gene sets.\r\n\r\nI'm checking for the separation of three sets of pathway pairs:\r\n\r\n* `IFN` - Type I and Type II interferon signaling pathways\r\n* `MYELOID` - neutrophil and monocyte/macrophage \r\n* `PROLIFERATION` - the G1 and G2 phases of the cell cycle (this is the one that'd I'd expect to be pretty difficult)\r\n\r\n**Figure, edited from the \"raw\" PDFs in this PR:**\r\n\r\n![pathway_separation_better_contrast](https://user-images.githubusercontent.com/19534205/50161069-c555b300-02a8-11e9-89c0-85fca40065fc.png)\r\n\r\n**Summary:**\r\n* For random subsampling, the larger the sample size, the better the pathway separation.\r\n* The biological conditions included in the training set matter! I would not expect `cell line` to perform particularly well, as these are unlikely to be mixtures of immune cells (generally speaking) or experiments where we expect the IFN signalling pathways to be probed outside of a handful of experiments.","created_at":"2018-12-16T17:32:01Z","updated_at":"2018-12-19T14:41:18Z","closed_at":"2018-12-19T14:41:18Z","merged_at":"2018-12-19T14:41:18Z","merge_commit_sha":"4ea0207a27ad1596d253c3d662edd7722b187f6a","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/greenelab/multi-plier/pulls/52/commits","review_comments_url":"https://api.github.com/repos/greenelab/multi-plier/pulls/52/comments","review_comment_url":"https://api.github.com/repos/greenelab/multi-plier/pulls/comments{/number}","comments_url":"https://api.github.com/repos/greenelab/multi-plier/issues/52/comments","statuses_url":"https://api.github.com/repos/greenelab/multi-plier/statuses/e9b5682ab98f3e9a5e3c8f5638ab88b75d2c11cb","head":{"label":"jaclyn-taroni:pathway-separation","ref":"pathway-separation","sha":"e9b5682ab98f3e9a5e3c8f5638ab88b75d2c11cb","user":{"login":"jaclyn-taroni","id":19534205,"node_id":"MDQ6VXNlcjE5NTM0MjA1","avatar_url":"https://avatars0.githubusercontent.com/u/19534205?v=4","gravatar_id":"","url":"https://api.github.com/users/jaclyn-taroni","html_url":"https://github.com/jaclyn-taroni","followers_url":"https://api.github.com/users/jaclyn-taroni/followers","following_url":"https://api.github.com/users/jaclyn-taroni/following{/other_user}","gists_url":"https://api.github.com/users/jaclyn-taroni/gists{/gist_id}","starred_url":"https://api.github.com/users/jaclyn-taroni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaclyn-taroni/subscriptions","organizations_url":"https://api.github.com/users/jaclyn-taroni/orgs","repos_url":"https://api.github.com/users/jaclyn-taroni/repos","events_url":"https://api.github.com/users/jaclyn-taroni/events{/privacy}","received_events_url":"https://api.github.com/users/jaclyn-taroni/received_events","type":"User","site_admin":false},"repo":{"id":157595177,"node_id":"MDEwOlJlcG9zaXRvcnkxNTc1OTUxNzc=","name":"multi-plier","full_name":"jaclyn-taroni/multi-plier","private":false,"owner":{"login":"jaclyn-taroni","id":19534205,"node_id":"MDQ6VXNlcjE5NTM0MjA1","avatar_url":"https://avatars0.githubusercontent.com/u/19534205?v=4","gravatar_id":"","url":"https://api.github.com/users/jaclyn-taroni","html_url":"https://github.com/jaclyn-taroni","followers_url":"https://api.github.com/users/jaclyn-taroni/followers","following_url":"https://api.github.com/users/jaclyn-taroni/following{/other_user}","gists_url":"https://api.github.com/users/jaclyn-taroni/gists{/gist_id}","starred_url":"https://api.github.com/users/jaclyn-taroni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaclyn-taroni/subscriptions","organizations_url":"https://api.github.com/users/jaclyn-taroni/orgs","repos_url":"https://api.github.com/users/jaclyn-taroni/repos","events_url":"https://api.github.com/users/jaclyn-taroni/events{/privacy}","received_events_url":"https://api.github.com/users/jaclyn-taroni/received_events","type":"User","site_admin":false},"html_url":"https://github.com/jaclyn-taroni/multi-plier","description":"A 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