{"id":60906,"date":"2024-09-12T16:51:42","date_gmt":"2024-09-12T08:51:42","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60906"},"modified":"2024-09-12T16:51:42","modified_gmt":"2024-09-12T08:51:42","slug":"%e4%bc%aa%e6%97%b6%e9%97%b4%e6%a6%82%e5%bf%b5%e4%b8%8e%e7%bb%86%e8%83%9e%e7%9a%84%e7%a9%ba%e9%97%b4%e4%bd%8d%e7%bd%ae%e7%9b%b8%e7%bb%93%e5%90%88%ef%bc%8cspaceflow%e5%8a%a9%e5%8a%9b%e6%8f%ad%e7%a4%ba","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60906","title":{"rendered":"\u4f2a\u65f6\u95f4\u6982\u5ff5\u4e0e\u7ec6\u80de\u7684\u7a7a\u95f4\u4f4d\u7f6e\u76f8\u7ed3\u5408\uff0cSpaceFlow\u52a9\u529b\u63ed\u793a\u7ec6\u80de\u7684\u65f6\u7a7a\u6a21\u5f0f"},"content":{"rendered":"\n<p><strong>\u524d\u8a00<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u54c8\u55bd\uff0c\u670b\u53cb\u4eec\u53c8\u89c1\u9762\u4e86\uff01\u4eca\u5929\u5b66\u4e60\u7684\u8fc7\u7a0b\u521d\u4e2d\u88ab\u4eba\u5de5\u667a\u80fd\u8d4b\u80fd\u4e86\u5417\uff1f\u5c0f\u4f19\u4f34\u4eec\u90fd\u77e5\u9053\u6df1\u5ea6\u5b66\u4e60\u6846\u67b6\u6700\u8fd1\u7206\u706b\uff0c\u50cf\u6211\u4eec\u719f\u6089\u7684\u56fe\u795e\u7ecf\u7f51\u7edc\u3001\u5377\u79ef\u795e\u7ecf\u7f51\u7edc\u7b49\u3002\u5c0f\u4f19\u4f34\u4eec\u6709\u6ca1\u6709\u60f3\u8fc7\u901a\u6df1\u5ea6\u5b66\u4e60\u6846\u67b6\u5c06\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u7eb3\u5165\u65f6\u7a7a\u4fe1\u606f\u4f1a\u6709\u54ea\u4e9b\u610f\u60f3\u4e0d\u5230\u7684\u60ca\u559c\u5462\uff1f\u5c06\u4f2a\u65f6\u95f4\u6982\u5ff5\u4e0e\u7ec6\u80de\u7684\u7a7a\u95f4\u4f4d\u7f6e\u76f8\u7ed3\u5408\uff0c\u5982\u4f55\u6765\u89e3\u5f00\u7ec6\u80de\u7684\u65f6\u7a7a\u683c\u5c40\uff1f\u5e26\u7740\u8fd9\u6837\u7684\u7591\u95ee\uff0c\u8ddf\u7740\u5927\u6d77\u54e5\u8d70\u8fdb\u4eca\u5929\u7684\u4e3b\u89d2\u2014\u2014&nbsp;SpaceFlow\u3002&nbsp;SpaceFlow\u901a\u8fc7\u5c06DGI\u6846\u67b6\u4e0e\u65e8\u5728\u6355\u83b7\u5c40\u90e8\u548c\u5168\u5c40\u7ed3\u6784\u6a21\u5f0f\u7684\u7a7a\u95f4\u6b63\u5219\u5316\u76f8\u7ed3\u5408\uff0c\u63d0\u53d6\u7a7a\u95f4\u4e00\u81f4\u7684\u4f4e\u7ef4\u5d4c\u5165\u5e76\u6784\u5efa\u4e86\u4f2a\u65f6\u7a7a\u56fe\uff08pSM\uff09\uff0c\u5b83\u4ee3\u8868\u4e86\u7f16\u7801\u7ec6\u80de\u4e4b\u95f4\u751f\u7269\u5b66\u5173\u7cfb\u7684\u7a7a\u95f4\u76f8\u5e72\u4f2a\u65f6\u95f4\u6392\u5e8f\uff0c\u4ee5\u53ca\u533a\u57df\u5206\u5272\u3002SpaceFlow \u88ab\u8bc1\u660e\u53ef\u4ee5\u4ea7\u751f\u5f3a\u5927\u7684\u57df\u5206\u5272\u5e76\u8bc6\u522b\u5177\u6709\u751f\u7269\u5b66\u610f\u4e49\u7684\u65f6\u7a7a\u6a21\u5f0f\u3002<\/p>\n\n\n\n<p>SpaceFlow \u662f\u7528\u4e8e\u4ece\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5b66 \uff08ST\uff09 \u6570\u636e\u4e2d\u8bc6\u522b\u65f6\u7a7a\u6a21\u5f0f\u548c\u7a7a\u95f4\u57df\u7684 Python \u5305\u3002SpaceFlow\u57fa\u4e8e\u6df1\u5ea6\u56fe\u7f51\u7edc\uff0c\u63d0\u4f9b\u4ee5\u4e0b\u529f\u80fd\uff1a<\/p>\n\n\n\n<ol type=\"1\">\n<li>\u5c06 ST \u6570\u636e\u7f16\u7801\u4e3a<strong>\u4f4e\u7ef4\u5d4c\u5165<\/strong>\uff0c\u4ee5\u53cd\u6620 ST \u6570\u636e\u4e2d\u7ec6\u80de\u7684\u8868\u8fbe\u76f8\u4f3c\u6027\u548c\u7a7a\u95f4\u90bb\u8fd1\u6027\u3002<\/li>\n\n\n\n<li>\u901a\u8fc7\u4ece\u5d4c\u5165\u6d3e\u751f\u7684<strong>\u4f2a\u65f6\u7a7a\u56fe \uff08pSM\uff09<\/strong>&nbsp;\u5408\u5e76 ST \u6570\u636e\u4e2d\u7ec6\u80de\u6216\u6591\u70b9\u7684<strong>\u65f6\u7a7a<\/strong>\u5173\u7cfb\u3002<\/li>\n\n\n\n<li>\u8bc6\u522b\u5177\u6709\u7a7a\u95f4\u8fde\u8d2f\u8868\u8fbe\u6a21\u5f0f<strong>\u7684\u7a7a\u95f4\u57df<\/strong>\u3002<\/li>\n<\/ol>\n\n\n\n<p>\u6709\u4ec0\u4e48\u751f\u4fe1\u5206\u6790\u4e0a\u7684\u95ee\u9898\u5927\u5bb6\u5c3d\u7ba1\u54a8\u8be2\u5927\u6d77\u54e5\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\u5927\u6d77\u54e5\u54e6\uff01\u7ec3\u4e86\u5341\u5e74\u751f\u4fe1\u5206\u6790\u7684\u5927\u6d77\u54e5\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<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"284\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-9.png?resize=640%2C284\" alt=\"\" class=\"wp-image-60907\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-9.png?w=900 900w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-9.png?resize=300%2C133 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-9.png?resize=768%2C341 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72471-9.png?resize=600%2C267 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u751f\u4fe1\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\u5927\u6d77\u54e5\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\u5927\u6d77\u54e5\uff0c\u4fdd\u8bc1\u670d\u52a1\u5668\u7684\u6027\u4ef7\u6bd4\u6700\u9ad8\u54e6<\/p>\n\n\n\n<p><strong>\u4ee3\u7801\u6559\u7a0b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u51c6\u5907\u76f8\u5173\u73af\u5883<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u8981\u5b89\u88c5 SpaceFlow\uff0c\u6211\u4eec\u5efa\u8bae\u4f7f\u7528 Anaconda Python \u53d1\u884c\u7248\u5e76\u521b\u5efa\u4e00\u4e2a\u9694\u79bb\u7684\u73af\u5883\uff0c\u4ee5\u4fbf SpaceFlow \u548c\u4f9d\u8d56\u9879\u4e0d\u4f1a\u4e0e\u5176\u4ed6\u5305\u6216\u5e94\u7528\u7a0b\u5e8f\u53d1\u751f\u51b2\u7a81\u6216\u5e72\u6270\u3002\u82e5\u8981\u521b\u5efa\u73af\u5883\uff0c\u8bf7\u5728\u547d\u4ee4\u884c\u4e2d\u8fd0\u884c\u4ee5\u4e0b\u811a\u672c\uff1a<\/p>\n\n\n\n<p>conda create -n spaceflow_env python=3.7<\/p>\n\n\n\n<p>\u521b\u5efa\u73af\u5883\u540e\uff0c\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u6fc0\u6d3b\u73af\u5883\uff1aspaceflow_env<\/p>\n\n\n\n<p>conda activate spaceflow_env<\/p>\n\n\n\n<p>pip install SpaceFlow<\/p>\n\n\n\n<p><strong>\u5bfc\u5165 SpaceFlow \u548c squidpy \u5305<\/strong><strong><\/strong><\/p>\n\n\n\n<p>import squidpy as sq<\/p>\n\n\n\n<p>import scanpy as sc<\/p>\n\n\n\n<p>from SpaceFlow import SpaceFlow<\/p>\n\n\n\n<p><strong>\u4ece squidpy \u5305\u52a0\u8f7d ST \u6570\u636e<\/strong><strong><\/strong><\/p>\n\n\n\n<p>adata = sq.datasets.seqfish()<\/p>\n\n\n\n<p>sc.pp.filter_genes(adata, min_cells=3)<\/p>\n\n\n\n<p><strong>\u521b\u5efa SpaceFlow \u5bf9\u8c61<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u4efb\u4e00\u5bf9\u8c61\u6216\u8ba1\u6570\u77e9\u9635\u521b\u5efa\u4e00\u4e2a SpaceFlow \u5bf9\u8c61\u4f5c\u4e3a\u8f93\u5165\uff1a<\/p>\n\n\n\n<p>sf = SpaceFlow.SpaceFlow(adata=adata)<\/p>\n\n\n\n<p>sf = SpaceFlow.SpaceFlow(count_matrix=adata.X, spatial_locs=adata.obsm[&#8216;spatial&#8217;], sample_names=adata.obs_names, gene_names=adata.var_names)<\/p>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>count_matrix\uff1a\u57fa\u56e0\u8868\u8fbe\u7684\u8ba1\u6570\u77e9\u9635\uff0c\u5927\u5c0f\uff08#\u4e2a\u7ec6\u80de\uff0c#\u4e2a\u57fa\u56e0\uff09\u76842Dnumpy\u6570\u7ec4\uff0c\u7c7b\u578b\u53ef\u9009numpy.ndarray<\/li>\n\n\n\n<li>spatial_locs\uff1a\u7ec6\u80de\uff08\u6216\u70b9\uff09\u7684\u7a7a\u95f4\u4f4d\u7f6e\u4e0e\u8ba1\u6570\u77e9\u9635\u7684\u884c\u5339\u914d\uff0c\u5927\u5c0f\u4e3a \uff08n_locations\uff0c\uff09 \u7684\u4e00\u7ef4 numpy \u6570\u7ec4\uff0c\u7c7b\u578b\u53ef\u9009numpy.ndarray<\/li>\n\n\n\n<li>sample_names\uff1a\u5927\u5c0f\u4e3a \uff08n_cells\uff0c\uff09 \u7684\u4e00\u7ef4 numpy str \u6570\u7ec4\u4e2d\u7684\u6837\u672c\u540d\u79f0\u5217\u8868<\/li>\n\n\n\n<li>gene_names\uff1a\u5927\u5c0f\u4e3a \uff08n_genes\uff0c\uff09 \u7684 1D numpy str \u6570\u7ec4\u4e2d\u7684\u57fa\u56e0\u540d\u79f0\u5217\u8868<\/li>\n<\/ul>\n\n\n\n<p><strong>\u5bf9ST\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u901a\u8fc7\u8fd0\u884c\u5bf9 ST \u6570\u636e\u8fdb\u884c\u9884\u5904\u7406\uff0c\u9884\u5904\u7406\u5305\u62ec\u8868\u8fbe\u8ba1\u6570\u77e9\u9635\u7684\u5f52\u4e00\u5316\u548c\u5bf9\u6570\u53d8\u6362\u3001\u9ad8\u53d8\u57fa\u56e0\u7684\u9009\u62e9\u4ee5\u53ca\u5229\u7528\u7a7a\u95f4\u5750\u6807\u6784\u5efa\u7a7a\u95f4\u90bb\u8fd1\u56fe\u3002\u8fd9\u91cc\u6211\u4eec\u4fdd\u7559\u524d3000\u4e2a\u9ad8\u53d8\u57fa\u56e0\u3002<\/p>\n\n\n\n<p>sf.preprocessing_data(n_top_genes=3000)<\/p>\n\n\n\n<p><strong>\u8bad\u7ec3\u6df1\u5ea6\u56fe\u7f51\u7edc\u6a21\u578b<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u7136\u540e\uff0c\u6211\u4eec\u8bad\u7ec3\u4e00\u4e2a\u7a7a\u95f4\u6b63\u5219\u5316\u7684\u6df1\u5ea6\u56fe\u7f51\u7edc\u6a21\u578b\uff0c\u4ee5\u5b66\u4e60\u4e00\u4e2a\u4f4e\u7ef4\u5d4c\u5165\uff0c\u8be5\u5d4c\u5165\u53cd\u6620\u4e86ST\u6570\u636e\u4e2d\u7ec6\u80de\u7684\u8868\u8fbe\u76f8\u4f3c\u6027\u548c\u7a7a\u95f4\u90bb\u8fd1\u6027\u3002<\/p>\n\n\n\n<p>sf.train(spatial_regularization_strength=0.1, z_dim=50, lr=1e-3, epochs=1000, max_patience=50, min_stop=100, random_seed=42, gpu=0, regularization_acceleration=True, edge_subset_sz=1000000)<\/p>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>spatial_regularization_strength\uff1a\u7a7a\u95f4\u6b63\u5219\u5316\u7684\u5f3a\u5ea6\u8d8a\u5927\uff0c\u6240\u8bc6\u522b\u7684\u7a7a\u95f4\u57df\u548c\u65f6\u7a7a\u683c\u5c40\u7684\u7a7a\u95f4\u8fde\u8d2f\u6027\u8d8a\u5927\u3002\uff08\u9ed8\u8ba4\u503c\uff1a0.1\uff09<\/li>\n\n\n\n<li>z_dim\uff1a\u5b66\u4e60\u5d4c\u5165\u7684\u76ee\u6807\u5927\u5c0f\u3002\uff08\u9ed8\u8ba4\u503c\uff1a50\uff09<\/li>\n\n\n\n<li>lr\uff1a\u4f18\u5316\u6a21\u578b\u7684\u5b66\u4e60\u7387\u3002\uff08\u9ed8\u8ba4\u503c\uff1a1E-3\uff09<\/li>\n\n\n\n<li>epochs\uff1a\u6a21\u578b\u8bad\u7ec3\u7684\u6700\u5927 epoch \u6570\u3002\uff08\u9ed8\u8ba4\u503c\uff1a1000\uff09<\/li>\n\n\n\n<li>max_patience\uff1a\u7b49\u5f85\u635f\u5931\u9012\u51cf\u7684\u6700\u5927\u7eaa\u5143\u6570\u3002\u5982\u679c\u5927\u4e8e\u6b64\u9608\u503c\u7684 epoch \u7684\u635f\u5931\u6ca1\u6709\u51cf\u5c11\uff0c\u5219\u5b66\u4e60\u5c06\u505c\u6b62\uff0c\u5e76\u4e14\u5177\u6709\u663e\u793a\u6700\u5c0f\u635f\u5931\u7684\u53c2\u6570\u7684\u6a21\u578b\u5c06\u4fdd\u7559\u4e3a\u6700\u4f73\u6a21\u578b\u3002\uff08\u9ed8\u8ba4\u503c\uff1a50\uff09<\/li>\n\n\n\n<li>min_stop\uff1a\u5982\u679c\u5927\u4e8e \u7684 epoch \u7684\u635f\u5931\u6ca1\u6709\u51cf\u5c11\uff0c\u5219\u5b66\u4e60\u53ef\u4ee5\u505c\u6b62\u7684\u6700\u65e9 epoch \u3002\uff08\u9ed8\u8ba4\u503c\uff1a100\uff09max_patience<\/li>\n\n\n\n<li>random_seed\uff1a\u8bbe\u7f6e\u4e3a \u3001 \u3001 \u5305\u7684\u968f\u673a\u751f\u6210\u5668\u7684\u968f\u673a\u79cd\u5b50\u3002\uff08\u9ed8\u8ba4\u503c\uff1a42\uff09randomnumpytorch<\/li>\n\n\n\n<li>gpu\uff1aNvidia GPU \u7684\u7d22\u5f15\uff0c\u5982\u679c\u6ca1\u6709 GPU\uff0c\u6a21\u578b\u5c06\u901a\u8fc7 CPU \u8fdb\u884c\u8bad\u7ec3\uff0c\u6bd4 GPU \u8bad\u7ec3\u65f6\u95f4\u6162\u3002\uff08\u9ed8\u8ba4\u503c\uff1a0\uff09<\/li>\n\n\n\n<li>regularization_acceleration\uff1a\u662f\u5426\u4f7f\u7528\u8fb9\u5b50\u96c6\u7b56\u7565\u52a0\u901f\u6b63\u5219\u5316\u635f\u5931\u7684\u8ba1\u7b97\uff08\u9ed8\u8ba4\u503c\uff1aTrue\uff09<\/li>\n\n\n\n<li>edge_subset_sz\uff1a\u7528\u4e8e\u6b63\u5219\u5316\u52a0\u901f\u7684\u8fb9\u7f18\u5b50\u96c6\u5927\u5c0f\uff08\u9ed8\u8ba4\u503c\uff1a1000000\uff09<\/li>\n<\/ul>\n\n\n\n<p><strong>ST\u6570\u636e\u7684\u9886\u57df\u5206\u5272<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6a21\u578b\u8bad\u7ec3\u5b8c\u6210\u540e\uff0c\u53ef\u4ee5\u901a\u8fc7sf.embedding\u8bbf\u95ee\u5b66\u4e60\u5230\u7684\u4f4e\u7ef4\u5d4c\u5165\u3002SpaceFlow \u5c06\u4f7f\u7528\u8fd9\u79cd\u5b66\u4e60\u5d4c\u5165\u6765\u8bc6\u522b\u57fa\u4e8e Leiden \u7b97\u6cd5\u7684\u7a7a\u95f4\u57df\u3002<\/p>\n\n\n\n<p>sf.segmentation(domain_label_save_filepath=&#8221;.\/domains.tsv&#8221;, n_neighbors=50, resolution=1.0)<\/p>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>domain_label_save_filepath\uff1a\u7528\u4e8e\u4fdd\u5b58\u5df2\u8bc6\u522b\u57df\u6807\u7b7e\u7684\u6587\u4ef6\u8def\u5f84\u3002\uff08\u9ed8\u8ba4\u503c\uff1a\u201c.\/domains.tsv\u201d\uff09<\/li>\n\n\n\n<li>n_neighbors\uff1a\u4f7f\u7528\u5d4c\u5165\u4f5c\u4e3a\u8f93\u5165\u6784\u5efa\u83b1\u987f\u56fe\u7684\u6bcf\u4e2a\u5355\u5143\u683c\u7684\u6700\u8fd1\u90bb\u5c45\u6570\u3002\uff08\u9ed8\u8ba4\u503c\uff1a50\uff09<\/li>\n\n\n\n<li>resolution\uff1a\u83b1\u987f\u805a\u7c7b\u7684\u5206\u8fa8\u7387\uff0c\u57df\u8d8a\u7c97\u8d8a\u5927\u3002\uff08\u9ed8\u8ba4\uff1a1.0\uff09<\/li>\n<\/ul>\n\n\n\n<p><strong>\u6ce8\u91ca\u548c\u8bc6\u522b\u7a7a\u95f4\u57df\u7684\u53ef\u89c6\u5316<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u4f7f\u7528\u5df2\u8bc6\u522b\u7684\u57df\u6807\u7b7e\u548c\u7ec6\u80de\u7684\u7a7a\u95f4\u5750\u6807\u7ed8\u5236\u7a7a\u95f4\u57df\u3002<\/p>\n\n\n\n<p>sf.plot_segmentation(segmentation_figure_save_filepath=&#8221;.\/domain_segmentation.pdf&#8221;, colormap=&#8221;tab20&#8243;, scatter_sz=1., rsz=4., csz=4., wspace=.4, hspace=.5, left=0.125, right=0.9, bottom=0.1, top=0.9)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"513\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72472-5.png?resize=640%2C513\" alt=\"\" class=\"wp-image-60908\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72472-5.png?w=773 773w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72472-5.png?resize=300%2C241 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72472-5.png?resize=768%2C616 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72472-5.png?resize=600%2C481 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>segmentation_figure_save_filepath\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1astr\uff0c\u7528\u4e8e\u4fdd\u5b58\u7a7a\u95f4\u57df\u53ef\u89c6\u5316\u56fe\u7684\u6587\u4ef6\u8def\u5f84\u3002\uff08\u9ed8\u8ba4\u503c\uff1a\u201c.\/domain_segmentation.pdf\u201d\uff09<\/li>\n\n\n\n<li>colormap\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1astr\uff0c\u4e0d\u540c\u57df\u7684\u989c\u8272\u56fe\uff0c\u5b8c\u6574\u7684\u989c\u8272\u56fe\u9009\u9879\u53c2\u89c1&nbsp;<a href=\"https:\/\/matplotlib.org\/3.5.1\/tutorials\/colors\/colormaps.html\"><u>matplotlib<\/u><\/a><\/li>\n\n\n\n<li>scatter_sz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u6807\u8bb0\u5927\u5c0f\uff08\u4ee5\u78c5\u4e3a\u5355\u4f4d\uff09\u3002\uff08\u9ed8\u8ba4\uff1a1.0\uff09<\/li>\n\n\n\n<li>rsz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1a\u6d6e\u70b9\u6570\uff0c\u56fe\u5f62\u7684\u884c\u5927\u5c0f\uff08\u4ee5\u82f1\u5bf8\u4e3a\u5355\u4f4d\uff09\uff0c\uff08\u9ed8\u8ba4\u503c\uff1a4.0\uff09<\/li>\n\n\n\n<li>csz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u56fe\u5f62\u7684\u5217\u5927\u5c0f\uff08\u4ee5\u82f1\u5bf8\u4e3a\u5355\u4f4d\uff09\uff0c\uff08\u9ed8\u8ba4\uff1a4.0\uff09<\/li>\n\n\n\n<li>wspace\uff1a \u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u4e3a\u5b50\u56fe\u4e4b\u95f4\u7684\u7a7a\u95f4\u4fdd\u7559\u7684\u5bbd\u5ea6\u91cf\uff0c\u8868\u793a\u4e3a\u5e73\u5747\u8f74\u5bbd\u5ea6\u7684\u5206\u6570\uff08\u9ed8\u8ba4\u503c\uff1a0.4\uff09<\/li>\n\n\n\n<li>hspace\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u4e3a\u5b50\u56fe\u4e4b\u95f4\u7684\u7a7a\u95f4\u4fdd\u7559\u7684\u9ad8\u5ea6\u91cf\uff0c\u8868\u793a\u4e3a\u5e73\u5747\u8f74\u9ad8\u5ea6\u7684\u5206\u6570\uff08\u9ed8\u8ba4\u503c\uff1a0.4\uff09<\/li>\n\n\n\n<li>left\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u56fe\u7684\u5b50\u56fe\u7684\u6700\u5de6\u8fb9\u4f4d\u7f6e\uff08\u4ee5\u5206\u6570\u8868\u793a\uff09\uff08\u9ed8\u8ba4\u503c\uff1a0.125\uff09<\/li>\n\n\n\n<li>right\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u56fe\u7684\u5b50\u56fe\u7684\u6700\u53f3\u8fb9\u4f4d\u7f6e\uff08\u4ee5\u5206\u6570\u8868\u793a\uff09\uff08\u9ed8\u8ba4\u503c\uff1a0.9\uff09<\/li>\n\n\n\n<li>bottom\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u56fe\u7684\u5b50\u56fe\u7684\u5e95\u90e8\u4f4d\u7f6e\uff08\u4ee5\u5206\u6570\u8868\u793a\uff09\uff08\u9ed8\u8ba4\u503c\uff1a0.1\uff09<\/li>\n\n\n\n<li>top\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u4ee5\u5206\u6570\u8868\u793a\u7684\u56fe\u5f62\u5b50\u56fe\u7684\u9876\u90e8\u4f4d\u7f6e\uff08\u9ed8\u8ba4\u503c\uff1a0.9\uff09<\/li>\n<\/ul>\n\n\n\n<p>import scanpy as sc<\/p>\n\n\n\n<p>sc.pl.spatial(adata, color=&#8221;celltype_mapped_refined&#8221;, spot_size=0.03)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"595\" height=\"261\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-7.png?resize=595%2C261\" alt=\"\" class=\"wp-image-60909\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-7.png?w=595 595w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72473-7.png?resize=300%2C132 300w\" sizes=\"(max-width: 595px) 100vw, 595px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>\u901a\u8fc7\u4f2a\u65f6\u7a7a\u56fe\uff08pSM\uff09\u8bc6\u522bST\u6570\u636e\u7684\u65f6\u7a7a\u683c\u5c40<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c06\u6269\u6563\u4f2a\u65f6\u95f4\uff08dpt\uff09\u7b97\u6cd5\u5e94\u7528\u4e8e\u5b66\u4e60\u5230\u7684\u7a7a\u95f4\u4e00\u81f4\u6027\u5d4c\u5165\uff0c\u4ee5\u751f\u6210\u4f2a\u65f6\u7a7a\u56fe\uff08pSM\uff09\u3002\u8be5 pSM \u4ee3\u8868\u7ec6\u80de\u7684\u7a7a\u95f4\u76f8\u5e72\u4f2a\u65f6\u95f4\u6392\u5e8f\uff0c\u5b83\u7f16\u7801\u7ec6\u80de\u4e4b\u95f4\u7684\u751f\u7269\u5b66\u5173\u7cfb\uff0c\u4f8b\u5982\u53d1\u80b2\u8f68\u8ff9\u548c\u764c\u75c7\u8fdb\u5c55\u3002<\/p>\n\n\n\n<p>sf.pseudo_Spatiotemporal_Map(pSM_values_save_filepath=&#8221;.\/pSM_values.tsv&#8221;, n_neighbors=20, resolution=1.0)<\/p>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>pSM_values_save_filepath\uff1a\u7528\u4e8e\u4fdd\u5b58\u63a8\u65ad\u7684 pSM \u503c\u7684\u6587\u4ef6\u8def\u5f84\u3002<\/li>\n\n\n\n<li>n_neighbors\uff1a\u4f7f\u7528\u5d4c\u5165\u4f5c\u4e3a\u8f93\u5165\u6784\u5efa\u83b1\u987f\u56fe\u7684\u6bcf\u4e2a\u7ec6\u80de\u7684\u6700\u8fd1\u90bb\u5c45\u6570\u3002\uff08\u9ed8\u8ba4\u503c\uff1a20\uff09<\/li>\n\n\n\n<li>resolution\uff1a\u83b1\u987f\u805a\u7c7b\u7684\u5206\u8fa8\u7387\uff0c\u57df\u8d8a\u7c97\u8d8a\u5927\u3002\uff08\u9ed8\u8ba4\uff1a1.0\uff09<\/li>\n<\/ul>\n\n\n\n<p><strong>\u8bc6\u522b\u7684\u4f2a\u65f6\u7a7a\u56fe\uff08pSM\uff09\u7684\u53ef\u89c6\u5316<\/strong><strong><\/strong><\/p>\n\n\n\n<p>sf.plot_pSM(pSM_figure_save_filepath=&#8221;.\/pseudo-Spatiotemporal-Map.pdf&#8221;, colormap=&#8221;roma&#8221;, scatter_sz=1., rsz=4., csz=4., wspace=.4, hspace=.5, left=0.125, right=0.9, bottom=0.1, top=0.9)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=640%2C640\" alt=\"\" class=\"wp-image-60910\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?w=800 800w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=300%2C300 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=150%2C150 150w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=768%2C768 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=600%2C600 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/09\/\u56fe\u72474-5.png?resize=100%2C100 100w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u53c2\u6570\uff1a<\/p>\n\n\n\n<ul>\n<li>pSM_figure_save_filepath\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1astr\uff0c\u7528\u4e8e\u4fdd\u5b58 pSM \u53ef\u89c6\u5316\u56fe\u7684\u6587\u4ef6\u8def\u5f84\u3002\uff08\u9ed8\u8ba4\u503c\uff1a\u201c.\/pseudo-Spatiotemporal-Map.pdf\u201d\uff09<\/li>\n\n\n\n<li>colormap\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1astr\uff0cpSM \u7684\u989c\u8272\u56fe\uff08\u9ed8\u8ba4\u503c\uff1a\u201croma\u201d\uff09\uff0c\u5b8c\u6574\u989c\u8272\u56fe\u9009\u9879\u8bf7\u53c2\u9605<a href=\"https:\/\/www.fabiocrameri.ch\/colourmaps-userguide\/\"><u>\u79d1\u5b66\u8272\u56fe<\/u><\/a><\/li>\n\n\n\n<li>scatter_sz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u6807\u8bb0\u5927\u5c0f\uff08\u4ee5\u78c5\u4e3a\u5355\u4f4d\uff09\u3002\uff08\u9ed8\u8ba4\uff1a1.0\uff09<\/li>\n\n\n\n<li>rsz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1a\u6d6e\u70b9\u6570\uff0c\u56fe\u5f62\u7684\u884c\u5927\u5c0f\uff08\u4ee5\u82f1\u5bf8\u4e3a\u5355\u4f4d\uff09\uff0c\uff08\u9ed8\u8ba4\u503c\uff1a4.0\uff09<\/li>\n\n\n\n<li>csz\uff1a\u53ef\u9009\uff0c\u7c7b\u578b\uff1afloat\uff0c\u56fe\u5f62\u7684\u5217\u5927\u5c0f\uff08\u4ee5\u82f1\u5bf8\u4e3a\u5355\u4f4d\uff09\uff0c\uff08\u9ed8\u8ba4\uff1a4.0\uff09<\/li>\n\n\n\n<li>wspace\uff1a 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