{"id":60845,"date":"2024-09-12T15:20:31","date_gmt":"2024-09-12T07:20:31","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60845"},"modified":"2024-09-12T15:20:31","modified_gmt":"2024-09-12T07:20:31","slug":"nat-methods%e9%a6%96%e5%8f%91-cellrank-%e4%ba%8c%e4%bb%a3%e7%89%88%e6%9c%ac%e5%bc%ba%e5%8a%bf%e4%b8%8a%e7%ba%bf%ef%bc%81%e6%96%b0%e6%a1%86%e6%9e%b6%e5%a6%82%e4%bd%95%e8%bf%9b%e8%a1%8c%e7%bb%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60845","title":{"rendered":"Nat. Methods\u9996\u53d1\u00a0| CellRank \u4e8c\u4ee3\u7248\u672c\u5f3a\u52bf\u4e0a\u7ebf\uff01\u65b0\u6846\u67b6\u5982\u4f55\u8fdb\u884c\u7ec6\u80de\u8f68\u8ff9\u5206\u6790\uff1f"},"content":{"rendered":"\n<p><strong>\u524d\u8a00<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u592a\u65e0\u8bed\u4e86\uff01\u6700\u8fd1\u5f88\u591a\u540c\u5b66\u5411\u5c0f\u679c\u62b1\u6028\uff0c\u521a\u521a\u5b66\u4f1a\u600e\u4e48\u4f7f\u7528CellRank\u8fdb\u884c\u7ec6\u80de\u8f68\u8ff9\u5206\u6790\uff0c\u7ed3\u679c\u53c8\u66f4\u65b0\u4e86\uff01\u5c0f\u679c\u4e3a\u4e86\u5b89\u629a\u5927\u5bb6\u7684\u60c5\u7eea\uff0c\u8d76\u7d27\u6487\u4e0b\u81ea\u5df1\u7684\u5b9e\u9a8c\uff0c\u9a6c\u4e0d\u505c\u8e44\u7684\u7ed9\u5927\u5bb6\u5949\u4e0a\u4e00\u4efd\u4f7f\u7528\u6559\u7a0b\uff01\u73b0\u6709\u7684\u8f68\u8ff9\u63a8\u65ad\u65b9\u6cd5\u4e3b\u8981\u8bbe\u8ba1\u7528\u4e8e\u5feb\u7167\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\uff0c\u65e0\u6cd5\u5bb9\u7eb3\u989d\u5916\u4fe1\u606f\uff0c\u5982\u5b9e\u9a8c\u65f6\u95f4\u70b9\u3001\u591a\u6a21\u6001\u6d4b\u91cf\u3001RNA\u901f\u5ea6\u548c\u4ee3\u8c22\u6807\u8bb0\u3002CellRank 2\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u3001\u53ef\u6269\u5c55\u7684\u6846\u67b6\uff0c\u7528\u4e8e\u7814\u7a76\u591a\u8fbe\u6570\u767e\u4e07\u7ec6\u80de\u7684\u591a\u89c6\u56fe\u5355\u7ec6\u80de\u6570\u636e\u4e2d\u7684\u7ec6\u80de\u547d\u8fd0\u3002\u901a\u8fc7\u5206\u79bb\u8f6c\u6362\u77e9\u9635\u7684\u63a8\u65ad\u548c\u5206\u6790\uff0cCellRank 2\u80fd\u591f\u4ee5\u4e00\u81f4\u548c\u7edf\u4e00\u7684\u65b9\u5f0f\u514b\u670d\u5355\u6570\u636e\u7c7b\u578b\u65b9\u6cd5\u7684\u5c40\u9650\u6027\u3002\u4e0b\u9762\u8d76\u5feb\u8ddf\u7740\u5c0f\u679c\u6765\u5b66\u4e60\u4e00\u4e0b\u5427\uff01\u6ca1\u6709\u65f6\u95f4\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u4eec\u4e5f\u4e0d\u8981\u7740\u6025\u54e6\uff01\u6709\u9700\u8981\u751f\u4fe1\u5206\u6790\u7684\u5c0f\u4f19\u4f34\u4eec\u4e5f\u53ef\u4ee5\u627e\u5c0f\u679c\u54e6\uff01\u7ec3\u4e86\u5341\u5e74\u751f\u4fe1\u5206\u6790\u7684\u5c0f\u679c\u5bf9\u4e8e\u751f\u4fe1\u5206\u6790\u77e5\u8bc6\u5df2\u7ecf\u5982\u9c7c\u5f97\u6c34\u4ece\u5206\u6790\u5230\u53ef\u89c6\u5316\u76f4\u5230\u4f60\u6ee1\u610f\u4e3a\u6b62\uff01<\/p>\n\n\n\n<p>CellRank2\u7684\u4e3b\u8981\u5e94\u7528\uff1a<\/p>\n\n\n\n<ul>\n<li>\u6839\u636e\u4e0d\u540c\u6570\u91cf\u7684\u751f\u7269\u5b66\u5148\u9a8c\uff08\u5305\u62ec\u4f2a\u65f6\u95f4\u3001\u53d1\u80b2\u6f5c\u529b\u3001RNA \u901f\u5ea6\uff09<\/li>\n\n\n\n<li>\u8ba1\u7b97\u521d\u59cb\u3001\u7ec8\u7aef\u548c\u4e2d\u95f4\u5b8f\u89c2\u72b6\u6001&nbsp;<\/li>\n\n\n\n<li>\u63a8\u65ad\u547d\u8fd0\u6982\u7387\u548c\u9a71\u52a8\u57fa\u56e0<\/li>\n\n\n\n<li>\u53ef\u89c6\u5316\u548c\u805a\u7c7b\u57fa\u56e0\u8868\u8fbe\u8d8b\u52bf<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"438\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?resize=640%2C438\" alt=\"\" class=\"wp-image-60846\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?resize=1024%2C700 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?resize=300%2C205 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?resize=768%2C525 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?resize=600%2C410 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-4.png?w=1277 1277w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5355\u7ec6\u80de\u6570\u636e\u5904\u7406\u8d77\u6765\u5360\u7528\u5185\u5b58\u5b9e\u5728\u592a\u5927\u4e86\uff0c\u653e\u8fc7\u81ea\u5df1\u7684\u7535\u8111\u5427\uff01\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u9001\u4e0a\u798f\u5229\u4e86\uff0c\u6709\u9700\u8981\u670d\u52a1\u5668\u7684\u5c0f\u4f19\u4f34\u4eec\uff0c\u6b22\u8fce\u5927\u5bb6\u8054\u7cfb\u5c0f\u679c\uff0c\u4fdd\u8bc1\u670d\u52a1\u5668\u7684\u6027\u4ef7\u6bd4\u6700\u9ad8\u54e6\uff01<\/p>\n\n\n\n<p><strong>\u4ee3\u7801\u6559\u7a0b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>1. \u5bfc\u5165\u5305\u548c\u6570\u636e<\/strong><strong><\/strong><\/p>\n\n\n\n<p>import sys<\/p>\n\n\n\n<p>if &#8220;google.colab&#8221; in sys.modules:<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;!pip install -q git+https:\/\/github.com\/theislab\/cellrank<\/p>\n\n\n\n<p>import cellrank as cr<\/p>\n\n\n\n<p>import scanpy as sc<\/p>\n\n\n\n<p>sc.settings.set_figure_params(frameon=False, dpi=100)<\/p>\n\n\n\n<p>cr.settings.verbosity = 2<\/p>\n\n\n\n<p>import warnings<\/p>\n\n\n\n<p>warnings.simplefilter(&#8220;ignore&#8221;, category=UserWarning)<\/p>\n\n\n\n<p>##\u6211\u4eec\u5c06\u4f7f\u7528\u4eba\u7c7b\u9aa8\u9ad3\u7684scRNA-seq\u6570\u636e\u96c6<\/p>\n\n\n\n<p>##\u6570\u636e\u83b7\u53d6\u5730\u5740\uff1a<em>https:\/\/data.humancellatlas.org\/explore\/projects\/091cf39b-01bc-42e5-9437-f419a66c8a45<\/em><em><\/em><\/p>\n\n\n\n<p>adata = cr.datasets.bone_marrow()<\/p>\n\n\n\n<p>adata<\/p>\n\n\n\n<p>##&nbsp;\u5c06MAGIC\u63d2\u8865\u6570\u636e\u79fb\u52a8\u5230 layers<\/p>\n\n\n\n<p>adata = adata[:, adata.var[&#8220;palantir&#8221;]].copy()<\/p>\n\n\n\n<p>adata.layers[&#8220;MAGIC_imputed_data&#8221;] = adata.obsm[&#8220;MAGIC_imputed_data&#8221;].copy()<\/p>\n\n\n\n<p><strong>2. \u9884\u5904\u7406\u6570\u636e<\/strong><strong><\/strong><\/p>\n\n\n\n<p>#\u8fc7\u6ee4\u548c\u89c4\u8303\u5316<\/p>\n\n\n\n<p>sc.pp.filter_genes(adata, min_cells=5)<\/p>\n\n\n\n<p>sc.pp.normalize_total(adata, target_sum=1e4)<\/p>\n\n\n\n<p>sc.pp.log1p(adata)<\/p>\n\n\n\n<p>sc.pp.highly_variable_genes(adata, n_top_genes=3000)<\/p>\n\n\n\n<p>#\u8ba1\u7b97&nbsp;PCA \u548c k \u6700\u8fd1\u90bb \uff08k-NN\uff09 \u56fe\u3002<\/p>\n\n\n\n<p>sc.tl.pca(adata, random_state=0)<\/p>\n\n\n\n<p>sc.pp.neighbors(adata, random_state=0)<\/p>\n\n\n\n<p>#\u4f7f\u7528\u539f\u59cb\u7814\u7a76\u63d0\u4f9b\u7684&nbsp;t-SNE \u5d4c\u5165\u3001\u805a\u7c7b\u6807\u7b7e\u548c Palantir \u4f2a\u65f6\u95f4\u53ef\u89c6\u5316\u8fd9\u4e9b\u6570\u636e<\/p>\n\n\n\n<p>sc.pl.embedding(adata, basis=&#8221;tsne&#8221;, color=[&#8220;clusters&#8221;, &#8220;palantir_pseudotime&#8221;])<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"286\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?resize=640%2C286\" alt=\"\" class=\"wp-image-60847\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?resize=1024%2C458 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?resize=300%2C134 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?resize=768%2C343 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?resize=600%2C268 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-3.png?w=1273 1273w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>3. \u4f7f\u7528\u5185\u6838<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u4e3a\u4e86\u6784\u9020\u4e00\u4e2a\u8fc7\u6e21\u77e9\u9635\uff0cCellRank \u5728 \u4e2d\u63d0\u4f9b\u4e86\u8bb8\u591a\u6838\u7c7b\u3002\u4e3a\u4e86\u6f14\u793a\u8fd9\u4e2a\u6982\u5ff5\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 k-NN \u56fe\u8fb9\u7f18\u6765\u6307\u5411\u589e\u52a0\u4f2a\u65f6\u95f4\u7684\u65b9\u5411<\/p>\n\n\n\n<p>from cellrank.kernels import PseudotimeKernel<\/p>\n\n\n\n<p>pk = PseudotimeKernel(adata, time_key=&#8221;palantir_pseudotime&#8221;)<\/p>\n\n\n\n<p>pk<\/p>\n\n\n\n<p>\u8bf7\u6ce8\u610f\uff0c\u5185\u6838\u9700\u8981\u4e00\u4e2a\u5bf9\u8c61\u6765\u4ece\u4e2d\u8bfb\u53d6\u6570\u636e&nbsp;&#8211; CellRank \u662f Scanpy\/AnnData \u751f\u6001\u7cfb\u7edf\u7684\u4e00\u90e8\u5206\u3002\u552f\u4e00\u7684\u4f8b\u5916\u662f\u5b83\u76f4\u63a5\u63a5\u53d7\u8f6c\u6362\u77e9\u9635\uff0c\u4ece\u800c\u53ef\u4ee5\u4ece scanpy\/AnnData \u4e16\u754c\u5916\u90e8\u8fde\u63a5\u5230 CellRank\u3002<\/p>\n\n\n\n<p>pk.compute_transition_matrix()<\/p>\n\n\n\n<p>pk<\/p>\n\n\n\n<p>\u4e3a\u4e86\u83b7\u5f97\u8be5\u6570\u636e\u96c6\u4e2d\u7ec6\u80de\u52a8\u529b\u5b66\u7684\u7b2c\u4e00\u5370\u8c61\uff0c\u6211\u4eec\u53ef\u4ee5\u4ece\u9020\u8840\u5e72\u7ec6\u80de&nbsp;\uff08HSC\uff09 \u5f00\u59cb\uff0c\u5728\u8fc7\u6e21\u57fa\u8d28\u9690\u542b\u7684\u9a6c\u5c14\u53ef\u592b\u94fe\u4e0a\u8fdb\u884c\u6a21\u62df\uff0c\u5e76\u5728 t-SNE \u5d4c\u5165\u4e2d\u53ef\u89c6\u5316\u8fd9\u4e9b\u7ec6\u80de\u3002<\/p>\n\n\n\n<p>pk.plot_random_walks(<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;seed=0,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;n_sims=100,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;start_ixs={&#8220;clusters&#8221;: &#8220;HSC_1&#8221;},<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;basis=&#8221;tsne&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;legend_loc=&#8221;right&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;dpi=150,<\/p>\n\n\n\n<p>)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"484\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?resize=640%2C484\" alt=\"\" class=\"wp-image-60848\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?resize=1024%2C775 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?resize=300%2C227 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?resize=768%2C581 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?resize=600%2C454 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-1.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u9ed1\u70b9\u548c\u9ec4\u70b9\u5206\u522b\u8868\u793a\u968f\u673a\u884c\u8d70\u5f00\u59cb\u548c\u7ec8\u7aef\u7ec6\u80de\u3002\u603b\u4f53\u800c\u8a00\uff0c\u8fd9\u53cd\u6620\u4e86\u4eba\u7c7b\u9020\u8840\u4e2d\u5df2\u77e5\u7684\u5206\u5316\u5c42\u6b21\u3002<\/p>\n\n\n\n<p><strong>4. \u5185\u6838\u6982\u8ff0<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6bcf\u79cd\u6a21\u5f0f\u548c\u751f\u7269\u7cfb\u7edf\u90fd\u6709\u5176\u81ea\u8eab\u7684\u4f18\u52bf\u548c\u5c40\u9650\u6027\uff0c\u56e0\u6b64\u4ed4\u7ec6\u9009\u62e9\u5185\u6838\u5f88\u91cd\u8981\u3002\u6211\u4eec\u5728\u4e0b\u56fe\u4e2d\u63d0\u4f9b\u4e86\u4e00\u4e9b\u6307\u5bfc\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"340\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?resize=640%2C340\" alt=\"\" class=\"wp-image-60850\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?resize=1024%2C544 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?resize=300%2C159 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?resize=768%2C408 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?resize=600%2C319 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72476-2.png?w=1266 1266w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5185\u6838\u9009\u62e9\u6307\u5357\uff1aCellRank\u5185\u6838\u652f\u6301\u4e0d\u540c\u7684\u6570\u636e\u6a21\u5f0f\u548c\u751f\u7269\u7cfb\u7edf\u3002\u6bcf\u4e2a\u90fd\u6709\u81ea\u5df1\u7684\u5047\u8bbe\u548c\u5c40\u9650\u6027\u3002<\/p>\n\n\n\n<p>\u5982\u679c\u60a8\u7684\u6570\u636e\u5df2\u7ecf\u6709\u4e00\u4e2a\u7ec6\u80de-\u7ec6\u80de\u8f6c\u6362\u77e9\u9635\uff0c\u5219\u53ef\u4ee5\u4f7f\u7528 CellRank \u7684\u63a5\u53e3\u4e0e\u5916\u90e8\u65b9\u6cd5\u76f4\u63a5\u4f20\u9012\u8be5\u77e9\u9635\u3002<\/p>\n\n\n\n<p>\u4efb\u4f55\u4e24\u4e2a\u5185\u6838\u90fd\u53ef\u4ee5\u901a\u8fc7\u52a0\u6743\u5e73\u5747\u503c\u8fdb\u884c\u5168\u5c40\u7ec4\u5408\u3002\u4e3a\u4e86\u8bc1\u660e\u8fd9\u4e00\u70b9\uff0c\u8ba9\u6211\u4eec\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u76f8\u4f3c\u6027\u8bbe\u7f6e\u4e00\u4e2a<\/p>\n\n\n\n<p>from cellrank.kernels import ConnectivityKernel<\/p>\n\n\n\n<p>ck = ConnectivityKernel(adata).compute_transition_matrix()<\/p>\n\n\n\n<p>ck<\/p>\n\n\n\n<p>##\u4e0e\u4e0a\u9762\u7684\u4f2a\u65f6\u95f4\u5185\u6838\u7ed3\u5408\u4f7f\u7528<\/p>\n\n\n\n<p>combined_kernel = 0.8 * pk + 0.2 * ck<\/p>\n\n\n\n<p>combined_kernel<\/p>\n\n\n\n<p><strong>5. \u5199\u5165\u548c\u8bfb\u53d6\u5185\u6838<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6709\u65f6\uff0c\u6211\u4eec\u53ef\u80fd\u5e0c\u671b\u5c06\u5185\u6838\u5199\u5165\u78c1\u76d8\uff0c\u4ee5\u4fbf\u7a0d\u540e\u7ee7\u7eed\u5206\u6790\uff0c\u6216\u8005\u5c06\u5176\u4f20\u9012\u7ed9\u5176\u4ed6\u4eba\u3002\u8fd9\u5f88\u5bb9\u6613\u505a\u5230;\u53ea\u9700\u5c06\u5185\u6838\u5199\u5165 adata\uff0c\u7136\u540e\u5c06 adata \u5199\u5165 file\uff1a<\/p>\n\n\n\n<p>pk.write_to_adata()<\/p>\n\n\n\n<p>adata.write(&#8220;hematopoiesis.h5ad&#8221;)<\/p>\n\n\n\n<p>#\u4e3a\u4e86\u7ee7\u7eed\u5206\u6790\uff0c\u6211\u4eec\u4ece\u78c1\u76d8\u8bfb\u53d6\u5bf9\u8c61\uff0c\u5e76\u4ece&nbsp;AnnData \u5bf9\u8c61\u521d\u59cb\u5316\u4e00\u4e2a\u65b0\u5185\u6838<\/p>\n\n\n\n<p>adata = sc.read(&#8220;hematopoiesis.h5ad&#8221;)<\/p>\n\n\n\n<p>pk_new = cr.kernels.PseudotimeKernel.from_adata(adata, key=&#8221;T_fwd&#8221;)<\/p>\n\n\n\n<p>pk_new<\/p>\n\n\n\n<p><strong>6. \u8bbe\u7f6e\u4f30\u7b97\u5668<\/strong><strong><\/strong><\/p>\n\n\n\n<p>from cellrank.estimators import GPCCA<\/p>\n\n\n\n<p>g = GPCCA(pk_new)<\/p>\n\n\n\n<p>print(g)<\/p>\n\n\n\n<p><strong>7. \u8bc6\u522b\u521d\u59cb\u548c\u7ed3\u675f\u72b6\u6001<\/strong><strong><\/strong><\/p>\n\n\n\n<p>g.fit(n_states=10, cluster_key=&#8221;clusters&#8221;)<\/p>\n\n\n\n<p>g.plot_macrostates(which=&#8221;all&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"623\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72477-1.png?resize=640%2C623\" alt=\"\" class=\"wp-image-60851\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72477-1.png?w=654 654w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72477-1.png?resize=300%2C292 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72477-1.png?resize=600%2C584 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>#\u5bf9\u4e8e\u6bcf\u4e2a\u5b8f\u72b6\u6001\uff0c\u8be5\u7b97\u6cd5\u4f1a\u8ba1\u7b97\u5173\u8054\u7684\u7a33\u5b9a\u6027\u503c\u3002<\/p>\n\n\n\n<p>g.predict_terminal_states(method=&#8221;top_n&#8221;, n_states=6)<\/p>\n\n\n\n<p>g.plot_macrostates(which=&#8221;terminal&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"624\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72478-1.png?resize=640%2C624\" alt=\"\" class=\"wp-image-60852\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72478-1.png?w=710 710w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72478-1.png?resize=300%2C292 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72478-1.png?resize=600%2C585 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>8. \u8ba1\u7b97\u547d\u8fd0\u6982\u7387\u548c\u9a71\u52a8\u57fa\u56e0<\/strong><strong><\/strong><\/p>\n\n\n\n<p>#\u6211\u4eec\u73b0\u5728\u53ef\u4ee5\u8ba1\u7b97\u6bcf\u4e2a\u7ec6\u80de\u8fbe\u5230\u6bcf\u4e2a\u7ec8\u7aef\u72b6\u6001\u7684\u53ef\u80fd\u6027\u3002<\/p>\n\n\n\n<p>g.compute_fate_probabilities()<\/p>\n\n\n\n<p>g.plot_fate_probabilities(legend_loc=&#8221;right&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"497\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724710-1.png?resize=640%2C497\" alt=\"\" class=\"wp-image-60853\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724710-1.png?w=891 891w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724710-1.png?resize=300%2C233 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724710-1.png?resize=768%2C596 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724710-1.png?resize=600%2C466 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u4e0a\u56fe\u7ed3\u5408\u4e86\u6240\u6709\u7ec8\u672b\u72b6\u6001\u7684\u547d\u8fd0\u6982\u7387\uff0c\u6bcf\u4e2a\u7ec6\u80de\u6839\u636e\u5176\u6700\u53ef\u80fd\u7684\u547d\u8fd0\u7740\u8272;\u989c\u8272\u5f3a\u5ea6\u53cd\u6620\u4e86\u8c31\u7cfb\u542f\u52a8\u7684\u7a0b\u5ea6\u3002<\/p>\n\n\n\n<p>cr.pl.circular_projection(adata, keys=&#8221;clusters&#8221;, legend_loc=&#8221;right&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"503\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724711-1.png?resize=640%2C503\" alt=\"\" class=\"wp-image-60854\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724711-1.png?w=966 966w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724711-1.png?resize=300%2C236 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724711-1.png?resize=768%2C603 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724711-1.png?resize=600%2C471 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6bcf\u4e2a\u70b9\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de\uff0c\u7531\u7c07\u6807\u7b7e\u7740\u8272\u3002\u7ec6\u80de\u6839\u636e\u5176\u547d\u8fd0\u6982\u7387\u6392\u5217\u5728\u5706\u5708\u5185;\u547d\u8fd0\u504f\u5411\u7684\u7ec6\u80de\u88ab\u653e\u7f6e\u5728\u5b83\u4eec\u76f8\u5e94\u7684\u89d2\u843d\u65c1\u8fb9\uff0c\u800c\u5e7c\u7a1a\u7684\u7ec6\u80de\u88ab\u653e\u7f6e\u5728\u4e2d\u95f4\u3002<\/p>\n\n\n\n<p>##\u4e3a\u4e86\u63a8\u65ad\u8fd9\u4e9b\u8f68\u8ff9\u4e2d\u7684\u4efb\u4f55\u4e00\u4e2a\u7684\u5047\u5b9a\u9a71\u52a8\u57fa\u56e0\uff0c\u6211\u4eec\u5c06\u8868\u8fbe\u503c\u4e0e\u547d\u8fd0\u6982\u7387\u76f8\u5173\u8054\u3002<\/p>\n\n\n\n<p>mono_drivers = g.compute_lineage_drivers(lineages=&#8221;Mono_1_1&#8243;)<\/p>\n\n\n\n<p>mono_drivers.head(10)<\/p>\n\n\n\n<p><strong>9. \u53ef\u89c6\u5316\u8868\u8fbe\u8d8b\u52bf<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u7ed9\u5b9a\u547d\u8fd0\u6982\u7387\u548c\u4f2a\u65f6\u95f4\uff0c\u6211\u4eec\u53ef\u4ee5\u7ed8\u5236\u8f68\u8ff9\u7279\u5f02\u6027\u57fa\u56e0\u8868\u8fbe\u8d8b\u52bf\u3002\u5177\u4f53\u6765\u8bf4\uff0c\u6211\u4eec\u62df\u5408\u5e7f\u4e49\u52a0\u6cd5\u6a21\u578b\uff08GAM\uff09\uff0c\u6839\u636e\u5176\u547d\u8fd0\u6982\u7387\u5411\u91cf\u5bf9\u6bcf\u4e2a\u7ec6\u80de\u7684\u8d21\u732e\u8fdb\u884c\u52a0\u6743\u3002<\/p>\n\n\n\n<p>model = cr.models.GAMR(adata)<\/p>\n\n\n\n<p>##\u521d\u59cb\u5316\u6a21\u578b\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u6cbf\u7740\u7279\u5b9a\u8f68\u8ff9\u53ef\u89c6\u5316\u57fa\u56e0\u52a8\u529b\u5b66\u3002<\/p>\n\n\n\n<p>cr.pl.gene_trends(<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;adata,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;model=model,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;data_key=&#8221;MAGIC_imputed_data&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;genes=[&#8220;GATA1&#8221;, &#8220;CD34&#8221;, &#8220;IRF8&#8221;, &#8220;MPO&#8221;],<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;same_plot=True,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;ncols=2,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;time_key=&#8221;palantir_pseudotime&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;hide_cells=True,<\/p>\n\n\n\n<p>)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"411\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?resize=640%2C411\" alt=\"\" class=\"wp-image-60855\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?resize=1024%2C658 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?resize=300%2C193 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?resize=768%2C493 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?resize=600%2C385 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724714.png?w=1267 1267w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5728\u4e0a\u9762\uff0c\u6211\u4eec\u6309\u57fa\u56e0\u5bf9\u8868\u8fbe\u8d8b\u52bf\u8fdb\u884c\u4e86\u5206\u7ec4\uff0c\u5e76\u53ef\u89c6\u5316\u4e86\u6bcf\u4e2a\u9762\u677f\u7684\u51e0\u4e2a\u8f68\u8ff9\u3002\u6211\u4eec\u4e5f\u53ef\u4ee5\u53cd\u8fc7\u6765\u505a&nbsp;&#8211; \u6309\u8f68\u8ff9\u5bf9\u8868\u8fbe\u8d8b\u52bf\u8fdb\u884c\u5206\u7ec4\uff0c\u6bcf\u4e2a\u9762\u677f\u53ef\u89c6\u5316\u51e0\u4e2a\u57fa\u56e0\u3002<\/p>\n\n\n\n<p>cr.pl.heatmap(<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;adata,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;model=model,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;data_key=&#8221;MAGIC_imputed_data&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;genes=[&#8220;GATA1&#8221;, &#8220;CD34&#8221;, &#8220;IRF8&#8221;, &#8220;MPO&#8221;],<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;lineages=[&#8220;Mono_1_1&#8221;, &#8220;Mega&#8221;, &#8220;CLP&#8221;],<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;time_key=&#8221;palantir_pseudotime&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;cbar=False,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;show_all_genes=True,<\/p>\n\n\n\n<p>)<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"147\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?resize=640%2C147\" alt=\"\" class=\"wp-image-60858\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?resize=1024%2C235 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?resize=300%2C69 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?resize=768%2C176 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?resize=600%2C138 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724716.png?w=1294 1294w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"142\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?resize=640%2C142\" alt=\"\" class=\"wp-image-60856\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?resize=1024%2C227 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?resize=300%2C67 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?resize=768%2C171 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?resize=600%2C133 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724715.png?w=1279 1279w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"142\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724717.png?resize=640%2C142\" alt=\"\" class=\"wp-image-60857\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u724717.png?resize=1024%2C227 1024w, 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