{"action":"created","comment":{"url":"https://api.github.com/repos/YosefLab/scVI/pulls/comments/197878375","pull_request_review_id":131708515,"id":197878375,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5Nzg3ODM3NQ==","diff_hunk":"@@ -1,32 +1,12 @@\n-import pandas as pd\n-import numpy as np\n+from .csv import CsvDataset\n \n-from .dataset import GeneExpressionDataset\n \n-\n-class CbmcDataset(GeneExpressionDataset):\n+class CbmcDataset(CsvDataset):\n     url = \"https://www.ncbi.nlm.nih.gov/geo/download/\" + \\\n           \"?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz\"\n \n     def __init__(self, save_path='data/'):\n-        self.save_path = save_path\n-\n-        # originally: GSE100866_CBMC_8K_13AB_10X-RNA_umi.csv.gz\n-\n-        self.download_name = 'cbmc.csv.gz'\n-\n-        expression_data, gene_names = self.download_and_preprocess()\n-\n-        super(CbmcDataset, self).__init__(\n-            *GeneExpressionDataset.get_attributes_from_matrix(\n-                expression_data), gene_names=gene_names)\n-\n-    def preprocess(self):\n-        print(\"Preprocessing cbmc data\")\n-        expression = pd.read_csv(self.save_path + self.download_name, index_col=0, compression='gzip').T\n-        gene_names = np.array(expression.columns, dtype=str)\n-\n-        selected = np.std(expression.values, axis=0).argsort()[-600:][::-1]\n-        expression_data = expression.values[:, selected]\n-\n-        return expression_data, gene_names\n+        super(CbmcDataset, self).__init__(filename='GSE100866_CBMC_8K_13AB_10X-RNA_umi.csv.gz',\n+                                          save_path=save_path,\n+                                          p_genes=600,","path":"scvi/dataset/cbmc.py","position":37,"original_position":37,"commit_id":"92ca6ed82aac8fb1c27c9c77ac4e47d8fa454bde","original_commit_id":"92ca6ed82aac8fb1c27c9c77ac4e47d8fa454bde","user":{"login":"imyiningliu","id":24255261,"node_id":"MDQ6VXNlcjI0MjU1MjYx","avatar_url":"https://avatars3.githubusercontent.com/u/24255261?v=4","gravatar_id":"","url":"https://api.github.com/users/imyiningliu","html_url":"https://github.com/imyiningliu","followers_url":"https://api.github.com/users/imyiningliu/followers","following_url":"https://api.github.com/users/imyiningliu/following{/other_user}","gists_url":"https://api.github.com/users/imyiningliu/gists{/gist_id}","starred_url":"https://api.github.com/users/imyiningliu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/imyiningliu/subscriptions","organizations_url":"https://api.github.com/users/imyiningliu/orgs","repos_url":"https://api.github.com/users/imyiningliu/repos","events_url":"https://api.github.com/users/imyiningliu/events{/privacy}","received_events_url":"https://api.github.com/users/imyiningliu/received_events","type":"User","site_admin":false},"body":"Do we also make 3000 the default value for `loom.py` (the same issue for `brain_small`)? ","created_at":"2018-06-25T17:31:22Z","updated_at":"2018-06-25T17:31:22Z","html_url":"https://github.com/YosefLab/scVI/pull/54#discussion_r197878375","pull_request_url":"https://api.github.com/repos/YosefLab/scVI/pulls/54","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/YosefLab/scVI/pulls/comments/197878375"},"html":{"href":"https://github.com/YosefLab/scVI/pull/54#discussion_r197878375"},"pull_request":{"href":"https://api.github.com/repos/YosefLab/scVI/pulls/54"}},"in_reply_to_id":197665137},"pull_request":{"url":"https://api.github.com/repos/YosefLab/scVI/pulls/54","id":196975249,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk2OTc1MjQ5","html_url":"https://github.com/YosefLab/scVI/pull/54","diff_url":"https://github.com/YosefLab/scVI/pull/54.diff","patch_url":"https://github.com/YosefLab/scVI/pull/54.patch","issue_url":"https://api.github.com/repos/YosefLab/scVI/issues/54","number":54,"state":"open","locked":false,"title":"Add CsvDataset and make CbmcDataset a subclass of CsvDataset ","user":{"login":"imyiningliu","id":24255261,"node_id":"MDQ6VXNlcjI0MjU1MjYx","avatar_url":"https://avatars3.githubusercontent.com/u/24255261?v=4","gravatar_id":"","url":"https://api.github.com/users/imyiningliu","html_url":"https://github.com/imyiningliu","followers_url":"https://api.github.com/users/imyiningliu/followers","following_url":"https://api.github.com/users/imyiningliu/following{/other_user}","gists_url":"https://api.github.com/users/imyiningliu/gists{/gist_id}","starred_url":"https://api.github.com/users/imyiningliu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/imyiningliu/subscriptions","organizations_url":"https://api.github.com/users/imyiningliu/orgs","repos_url":"https://api.github.com/users/imyiningliu/repos","events_url":"https://api.github.com/users/imyiningliu/events{/privacy}","received_events_url":"https://api.github.com/users/imyiningliu/received_events","type":"User","site_admin":false},"body":"I also fixed styles so that the parameter names for the generic Datasets (`CsvDataset`, `LoomDataset` and `Dataset10X`) are more consistent. 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