{"action":"created","issue":{"url":"https://api.github.com/repos/satijalab/seurat/issues/177","repository_url":"https://api.github.com/repos/satijalab/seurat","labels_url":"https://api.github.com/repos/satijalab/seurat/issues/177/labels{/name}","comments_url":"https://api.github.com/repos/satijalab/seurat/issues/177/comments","events_url":"https://api.github.com/repos/satijalab/seurat/issues/177/events","html_url":"https://github.com/satijalab/seurat/issues/177","id":265544982,"number":177,"title":"Error running BuildClusterTree using SNN","user":{"login":"yueqiw","id":5046690,"avatar_url":"https://avatars0.githubusercontent.com/u/5046690?v=4","gravatar_id":"","url":"https://api.github.com/users/yueqiw","html_url":"https://github.com/yueqiw","followers_url":"https://api.github.com/users/yueqiw/followers","following_url":"https://api.github.com/users/yueqiw/following{/other_user}","gists_url":"https://api.github.com/users/yueqiw/gists{/gist_id}","starred_url":"https://api.github.com/users/yueqiw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yueqiw/subscriptions","organizations_url":"https://api.github.com/users/yueqiw/orgs","repos_url":"https://api.github.com/users/yueqiw/repos","events_url":"https://api.github.com/users/yueqiw/events{/privacy}","received_events_url":"https://api.github.com/users/yueqiw/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-10-15T04:28:23Z","updated_at":"2018-03-01T23:36:19Z","closed_at":"2018-03-01T23:36:19Z","author_association":"CONTRIBUTOR","body":"Hi,\r\n\r\nI was using `BuildClusterTree()` to build a tree of my clustering result as described in the pbmc33k tutorial. When I try to build a tree based on SNN graph connectivity between clusters, I got the following error:\r\n\r\n```\r\numi_seurat <- umi_seurat %>% BuildClusterTree(SNN.use = umi_seurat@snn)\r\n\r\nError in WhichCells(object = object, ident = j) : Identity : 28 not found.\r\n```\r\nI have 28 clusters in the `@ident` slot. Looking at the source code, I think the problem is because the `FindClusters()` gives indices that start from 0 (0, 1, ..., 27), but `BuildClusterTree()` looks for cluster indices that start from 1 (1, 2, ..., 28). The error can be resolved by resetting the `@ident` slot to (1, 2, ... 28). "},"comment":{"url":"https://api.github.com/repos/satijalab/seurat/issues/comments/369769248","html_url":"https://github.com/satijalab/seurat/issues/177#issuecomment-369769248","issue_url":"https://api.github.com/repos/satijalab/seurat/issues/177","id":369769248,"user":{"login":"satijalab","id":8411851,"avatar_url":"https://avatars1.githubusercontent.com/u/8411851?v=4","gravatar_id":"","url":"https://api.github.com/users/satijalab","html_url":"https://github.com/satijalab","followers_url":"https://api.github.com/users/satijalab/followers","following_url":"https://api.github.com/users/satijalab/following{/other_user}","gists_url":"https://api.github.com/users/satijalab/gists{/gist_id}","starred_url":"https://api.github.com/users/satijalab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/satijalab/subscriptions","organizations_url":"https://api.github.com/users/satijalab/orgs","repos_url":"https://api.github.com/users/satijalab/repos","events_url":"https://api.github.com/users/satijalab/events{/privacy}","received_events_url":"https://api.github.com/users/satijalab/received_events","type":"User","site_admin":false},"created_at":"2018-03-01T23:36:19Z","updated_at":"2018-03-01T23:36:19Z","author_association":"OWNER","body":"Issue has been fixed on develop branch, will be in the next CRAN release"}}
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