{"action":"created","issue":{"url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/128","repository_url":"https://api.github.com/repos/maximilianh/cellBrowser","labels_url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/128/comments","events_url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/128/events","html_url":"https://github.com/maximilianh/cellBrowser/issues/128","id":480361041,"node_id":"MDU6SXNzdWU0ODAzNjEwNDE=","number":128,"title":"Error when trying to recalculate markers","user":{"login":"matthewspeir","id":11509990,"node_id":"MDQ6VXNlcjExNTA5OTkw","avatar_url":"https://avatars3.githubusercontent.com/u/11509990?v=4","gravatar_id":"","url":"https://api.github.com/users/matthewspeir","html_url":"https://github.com/matthewspeir","followers_url":"https://api.github.com/users/matthewspeir/followers","following_url":"https://api.github.com/users/matthewspeir/following{/other_user}","gists_url":"https://api.github.com/users/matthewspeir/gists{/gist_id}","starred_url":"https://api.github.com/users/matthewspeir/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthewspeir/subscriptions","organizations_url":"https://api.github.com/users/matthewspeir/orgs","repos_url":"https://api.github.com/users/matthewspeir/repos","events_url":"https://api.github.com/users/matthewspeir/events{/privacy}","received_events_url":"https://api.github.com/users/matthewspeir/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2019-08-13T20:47:21Z","updated_at":"2019-09-04T14:50:03Z","closed_at":null,"author_association":"COLLABORATOR","body":"When trying to recalculate the markers for a dataset, I get the following error:\r\n```\r\nINFO:root:Finding top markers for each cluster\r\nTraceback (most recent call last):\r\n  File \"/cluster/home/mspeir/miniconda3/bin/cbScanpy\", line 10, in <module>\r\n    sys.exit(cbScanpyCli())\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/cellbrowser/cellbrowser.py\", line 4680, in cbScanpyCli\r\n    adata, params = cbScanpy(matrixFname, metaFname, inCluster, confFname, figDir, logFname)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/cellbrowser/cellbrowser.py\", line 4525, in cbScanpy\r\n    sc.tl.rank_genes_groups(adata, clusterField)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/scanpy/tools/_rank_genes_groups.py\", line 119, in rank_genes_groups\r\n    adata, groups_order, groupby)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/scanpy/utils.py\", line 649, in select_groups\r\n    groups_order = adata.obs[key].cat.categories\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/generic.py\", line 4368, in __getattr__\r\n    return object.__getattribute__(self, name)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/accessor.py\", line 133, in __get__\r\n    accessor_obj = self._accessor(obj)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py\", line 2378, in __init__\r\n    self._validate(data)\r\n  File \"/cluster/home/mspeir/miniconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py\", line 2387, in _validate\r\n    raise AttributeError(\"Can only use .cat accessor with a \"\r\nAttributeError: Can only use .cat accessor with a 'category' dtype\r\n```\r\nCommand:\r\n```\r\ncbScanpy -e exprMatrix.tsv.gz -m meta.tsv -o tms-bat-facs_marker-recalc -n tms-bat-facs --inCluster 'Louvain Cluster'\r\n```\r\nFiles:\r\n```\r\n/hive/data/inside/cells/datasets/tabula-muris-senis/tms-bat-facs\r\n```\r\n\r\n(Also is it really using the input clusters to recalc the marker genes? I see this in the output which makes me think it's not: `INFO:root:Found 22 louvain clusters`...)\r\n"},"comment":{"url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/comments/527936211","html_url":"https://github.com/maximilianh/cellBrowser/issues/128#issuecomment-527936211","issue_url":"https://api.github.com/repos/maximilianh/cellBrowser/issues/128","id":527936211,"node_id":"MDEyOklzc3VlQ29tbWVudDUyNzkzNjIxMQ==","user":{"login":"matthewspeir","id":11509990,"node_id":"MDQ6VXNlcjExNTA5OTkw","avatar_url":"https://avatars3.githubusercontent.com/u/11509990?v=4","gravatar_id":"","url":"https://api.github.com/users/matthewspeir","html_url":"https://github.com/matthewspeir","followers_url":"https://api.github.com/users/matthewspeir/followers","following_url":"https://api.github.com/users/matthewspeir/following{/other_user}","gists_url":"https://api.github.com/users/matthewspeir/gists{/gist_id}","starred_url":"https://api.github.com/users/matthewspeir/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthewspeir/subscriptions","organizations_url":"https://api.github.com/users/matthewspeir/orgs","repos_url":"https://api.github.com/users/matthewspeir/repos","events_url":"https://api.github.com/users/matthewspeir/events{/privacy}","received_events_url":"https://api.github.com/users/matthewspeir/received_events","type":"User","site_admin":false},"created_at":"2019-09-04T14:50:03Z","updated_at":"2019-09-04T14:50:03Z","author_association":"COLLABORATOR","body":"Thanks, Max!\r\n\r\nWhen you say \"it didn't happen for the other datasets...\", did you use the 'Louvain Cluster' field as the cluster field? Looking at the FACS bladder dataset, it looks like you used the 'free_annotation' field rather than the 'Louvain Cluster' field. I thought we were going with the Louvain Cluster field for the label, not cell type."}}
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