{"id":61606,"date":"2024-11-19T15:31:07","date_gmt":"2024-11-19T07:31:07","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=61606"},"modified":"2026-09-11T18:47:18","modified_gmt":"2026-09-11T10:47:18","slug":"%e5%8d%95%e7%bb%86%e8%83%9e%e4%b9%8b%e6%89%be%e5%af%bb%e5%8f%97%e5%bd%b1%e5%93%8d%e6%9c%80%e5%a4%a7%e7%9a%84%e7%bb%86%e8%83%9e%e7%b1%bb%e5%9e%8b%ef%bc%8caugur%e6%9d%a5%e5%b8%ae%e5%bf%99%e5%95%a6","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/%e5%8d%95%e7%bb%86%e8%83%9e%e4%b9%8b%e6%89%be%e5%af%bb%e5%8f%97%e5%bd%b1%e5%93%8d%e6%9c%80%e5%a4%a7%e7%9a%84%e7%bb%86%e8%83%9e%e7%b1%bb%e5%9e%8b%ef%bc%8caugur%e6%9d%a5%e5%b8%ae%e5%bf%99%e5%95%a6\/","title":{"rendered":"\u7528 Augur \u627e\u5230\u53d7\u6270\u52a8\u5f71\u54cd\u6700\u5927\u7684\u7ec6\u80de\u7c7b\u578b"},"content":{"rendered":"\n
\n

Augur \u80fd\u89e3\u51b3\u4ec0\u4e48\u95ee\u9898<\/h2>\n

\u5b8c\u6210\u5355\u7ec6\u80de\u805a\u7c7b\u548c\u6ce8\u91ca\u540e\uff0c\u4e00\u4e2a\u5e38\u89c1\u95ee\u9898\u662f\uff1a\u63a5\u4e0b\u6765\u5e94\u8be5\u91cd\u70b9\u7814\u7a76\u54ea\u4e00\u79cd\u7ec6\u80de\uff1f<\/strong>\u4ec5\u6bd4\u8f83\u7ec6\u80de\u6bd4\u4f8b\uff0c\u6709\u65f6\u4e0d\u8db3\u4ee5\u53cd\u6620\u4e0d\u540c\u5b9e\u9a8c\u6761\u4ef6\u5bf9\u7ec6\u80de\u72b6\u6001\u9020\u6210\u7684\u5f71\u54cd\u3002<\/p>\n

Augur \u7528\u4e8e\u8bc6\u522b\u5bf9\u751f\u7269\u6270\u52a8\u6700\u654f\u611f\u7684\u7ec6\u80de\u7c7b\u578b\u3002\u8fd9\u91cc\u7684\u201c\u6270\u52a8\u201d\u53ef\u4ee5\u662f\u8870\u8001\u4e0e\u5e74\u8f7b\u3001\u6cbb\u7597\u4e0e\u5bf9\u7167\u3001\u75be\u75c5\u4e0e\u5065\u5eb7\uff0c\u4e5f\u53ef\u4ee5\u662f\u5176\u4ed6\u5177\u6709\u660e\u786e\u5206\u7ec4\u7684\u5b9e\u9a8c\u6761\u4ef6\u3002<\/p>\n

\n
\u8870\u8001\u7814\u7a76<\/b>\u6bd4\u8f83\u5e74\u8f7b\u4e0e\u8870\u8001\u6837\u672c\uff0c\u7b5b\u9009\u54cd\u5e94\u6700\u660e\u663e\u7684\u7ec6\u80de\u7c7b\u578b\u3002<\/span><\/div>\n
\u75be\u75c5\u7814\u7a76<\/b>\u6bd4\u8f83\u5065\u5eb7\u4e0e\u75be\u75c5\u72b6\u6001\uff0c\u786e\u5b9a\u4f18\u5148\u6df1\u5165\u5206\u6790\u7684\u7ec6\u80de\u7fa4\u3002<\/span><\/div>\n
\u6cbb\u7597\u7814\u7a76<\/b>\u6bd4\u8f83\u6cbb\u7597\u4e0e\u5bf9\u7167\u6837\u672c\uff0c\u8bc4\u4f30\u54ea\u4e9b\u7ec6\u80de\u5bf9\u5e72\u9884\u6700\u654f\u611f\u3002<\/span><\/div>\n <\/div>\n
\u8ba1\u7b97\u8d44\u6e90\u63d0\u9192\uff1a<\/strong>\u7ec6\u80de\u6570\u91cf\u8f83\u591a\u65f6\uff0cAugur \u7684\u91cd\u590d\u62bd\u6837\u548c\u6a21\u578b\u8bad\u7ec3\u4f1a\u5360\u7528\u8f83\u591a\u5185\u5b58\u4e0e CPU\u3002\u5efa\u8bae\u5148\u7528\u5c0f\u6837\u672c\u9a8c\u8bc1\u6d41\u7a0b\uff0c\u518d\u6839\u636e\u6570\u636e\u89c4\u6a21\u9009\u62e9\u5de5\u4f5c\u7ad9\u6216\u670d\u52a1\u5668\u3002<\/div>\n<\/section>\n\n
\n

\u6587\u732e\u4e2d\u7684\u5e94\u7528<\/h2>\n

\u4e0b\u9762\u4e24\u9879\u7814\u7a76\u90fd\u4f7f\u7528\u4e86\u7ec6\u80de\u7c7b\u578b\u4f18\u5148\u7ea7\u5206\u6790\uff0c\u7528\u6765\u5224\u65ad\u54ea\u4e9b\u7ec6\u80de\u5bf9\u8870\u8001\u6700\u654f\u611f\u3002\u539f\u6587\u622a\u56fe\u4fdd\u6301\u539f\u59cb\u5c3a\u5bf8\u5c55\u793a\uff0c\u907f\u514d\u4f4e\u5206\u8fa8\u7387\u56fe\u7247\u88ab\u5f3a\u884c\u62c9\u4f38\u3002<\/p>\n

\n
\n
\"\u7075\u957f\u7c7b\u809d\u810f\u8870\u8001\u7814\u7a76\u4e2d\u4f7f\u7528<\/div>\n
\u6848\u4f8b 01 \u00b7 \u809d\u810f\u8870\u8001<\/small>

\u809d\u7ec6\u80de Hep \u54cd\u5e94\u6700\u660e\u663e<\/h3>

\u7814\u7a76\u6307\u51fa\uff0c\u5728\u5355\u6838\u8f6c\u5f55\u7ec4\u6570\u636e\u4e2d\uff0cHep \u662f\u5bf9\u8870\u8001\u53cd\u5e94\u6700\u663e\u8457\u7684\u7ec6\u80de\u7c7b\u578b\u3002<\/p><\/div>\n <\/article>\n

\n
\"\u7075\u957f\u7c7b\u5fc3\u810f\u8870\u8001\u7814\u7a76\u4e2d\u4f7f\u7528<\/div>\n
\u6848\u4f8b 02 \u00b7 \u5fc3\u810f\u8870\u8001<\/small>

\u5fc3\u808c\u7ec6\u80de CM \u53d7\u5f71\u54cd\u6700\u5927<\/h3>

\u7814\u7a76\u5c06 CM \u8bc6\u522b\u4e3a\u5fc3\u810f\u8870\u8001\u8fc7\u7a0b\u4e2d\u53d7\u5f71\u54cd\u6700\u660e\u663e\u7684\u7ec6\u80de\u7c7b\u578b\u3002<\/p><\/div>\n <\/article>\n <\/div>\n<\/section>\n\n

\n

\u5b89\u88c5 Augur<\/h2>\n

Augur \u4f9d\u8d56\u4e00\u7ec4\u6570\u636e\u5904\u7406\u3001\u5efa\u6a21\u548c\u5e76\u884c\u8ba1\u7b97\u5305\u3002\u9996\u6b21\u5b89\u88c5\u524d\uff0c\u8bf7\u786e\u8ba4 R \u73af\u5883\u53ef\u4ee5\u6b63\u5e38\u8fde\u63a5 CRAN \u548c GitHub\u3002\u4ee5\u4e0b\u547d\u4ee4\u5df2\u4e0e Augur \u5b98\u65b9\u8bf4\u660e<\/a>\u6838\u5bf9\u3002<\/p>\n

\u4e3b\u8981\u4f9d\u8d56<\/h3>\n
    \n
  • dplyr \u2265 0.8.0<\/li>
  • purrr \u2265 0.3.2<\/li>
  • tibble \u2265 2.1.3<\/li>
  • magrittr \u2265 1.5<\/li>
  • Matrix \u2265 1.2-14<\/li>
  • sparseMatrixStats \u2265 0.1.0<\/li>
  • parsnip \u2265 0.0.2<\/li>
  • recipes \u2265 0.1.4<\/li>
  • rsample \u2265 0.0.4<\/li>
  • yardstick \u2265 0.0.3<\/li>
  • pbmcapply \u2265 1.5.0<\/li>
  • lmtest \u2265 0.9-37<\/li>
  • rlang \u2265 0.4.0<\/li>
  • glmnet \u2265 2.0<\/li>
  • randomForest \u2265 4.6-14<\/li>\n <\/ul>\n
    \n
    R \u00b7 \u5b89\u88c5\u547d\u4ee4<\/span><\/div>\n 
    install.packages<\/span>(\"devtools\"<\/span>)\n\ndevtools::install_github<\/span>(\"Bioconductor\/MatrixGenerics\"<\/span>)\ndevtools::install_github<\/span>(\"const-ae\/sparseMatrixStats\"<\/span>)\ndevtools::install_github<\/span>(\"neurorestore\/Augur\"<\/span>)\n\nlibrary<\/span>(Augur)<\/code><\/pre>\n  <\/div>\n  
    \u590d\u5236\u53ef\u76f4\u63a5\u8fd0\u884c\uff1a<\/strong>\u539f\u6587\u4e2d\u7684\u4e2d\u6587\u5f2f\u5f15\u53f7\u5df2\u6539\u4e3a\u82f1\u6587\u534a\u89d2\u5f15\u53f7\uff0c\u51cf\u5c11\u7c98\u8d34\u5230 R \u63a7\u5236\u53f0\u540e\u7684\u8bed\u6cd5\u9519\u8bef\u3002<\/div>\n<\/section>\n\n
    \n  
    \u8fd0\u884c\u793a\u4f8b<\/h2>\n  
    \u8fd9\u91cc\u4f7f\u7528 Augur \u81ea\u5e26\u7684 sc_sim<\/code> \u793a\u4f8b\u6570\u636e\u3002\u5143\u6570\u636e\u5305\u542b\u4e24\u5217\uff1alabel<\/code> \u8868\u793a treatment \u6216 control\uff0ccell_type<\/code> \u8868\u793a\u7ec6\u80de\u7c7b\u578b\u3002<\/p>\n  
    \n    
    R \u00b7 \u67e5\u770b\u793a\u4f8b\u6570\u636e<\/span><\/div>\n    
    data<\/span>(\"sc_sim\"<\/span>)\nhead<\/span>(sc_sim@meta.data)<\/code><\/pre>\n  <\/div>\n  
    \n    
    \u8fd0\u884c\u7ed3\u679c<\/div>\n    
          label cell_type\n1   control CellTypeA\n2 treatment CellTypeA\n3 treatment CellTypeA\n4   control CellTypeA\n5   control CellTypeA\n6 treatment CellTypeA<\/code><\/pre>\n  <\/div>\n\n  
    \u8ba1\u7b97\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u7684 AUC<\/h3>\n  
    \u8fd0\u884c calculate_auc()<\/code> \u540e\uff0c\u67e5\u770b\u7ed3\u679c\u5bf9\u8c61\u4e2d\u7684 AUC<\/code> \u8868\u3002<\/p>\n  
    \n    
    R \u00b7 \u8ba1\u7b97\u4f18\u5148\u7ea7<\/span><\/div>\n    
    augur_result <- calculate_auc<\/span>(sc_sim)\naugur_result$AUC<\/code><\/pre>\n  <\/div>\n  
    \n    
    \u4e00\u6b21\u793a\u4f8b\u8fd0\u884c\u7ed3\u679c<\/div>\n    
    # A tibble: 3 \u00d7 2\n  cell_type   auc\n  <chr>     <dbl>\n1 CellTypeC 0.879\n2 CellTypeB 0.747\n3 CellTypeA 0.554<\/code><\/pre>\n  <\/div>\n  
    1<\/span>
    \u7ed3\u679c\u89e3\u8bfb\uff1a<\/strong>CellTypeC \u7684 AUC \u6700\u9ad8\uff0c\u5176\u6b21\u662f CellTypeB \u548c CellTypeA\u3002\u56e0\u6b64\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0cCellTypeC \u662f\u66f4\u503c\u5f97\u4f18\u5148\u5173\u6ce8\u7684\u7ec6\u80de\u7c7b\u578b\u3002<\/p><\/div>\n  
    \u6570\u503c\u53ef\u80fd\u7565\u6709\u6ce2\u52a8\uff1a<\/strong>Augur \u5305\u542b\u91cd\u590d\u62bd\u6837\u548c\u6a21\u578b\u8bad\u7ec3\uff1b\u8f6f\u4ef6\u7248\u672c\u3001\u968f\u673a\u79cd\u5b50\u548c\u8fd0\u884c\u73af\u5883\u4e0d\u540c\uff0cAUC \u7684\u5c0f\u6570\u503c\u53ef\u80fd\u4e0e\u793a\u4f8b\u7565\u6709\u5dee\u5f02\uff0c\u4f46\u4f18\u5148\u7ea7\u5224\u65ad\u901a\u5e38\u5e94\u4fdd\u6301\u7a33\u5b9a\u3002<\/div>\n<\/section>\n\n
    \n  
    \u53ef\u89c6\u5316 AUC \u7ed3\u679c<\/h2>\n  
    \u7ec6\u80de\u7c7b\u578b\u6570\u91cf\u8f83\u5c11\u65f6\uff0c\u6a2a\u5411\u6761\u5f62\u56fe\u901a\u5e38\u6bd4\u73af\u5f62\u56fe\u66f4\u5bb9\u6613\u6bd4\u8f83\u5dee\u5f02\uff1b\u7ec6\u80de\u7c7b\u578b\u8f83\u591a\u65f6\uff0c\u518d\u6839\u636e\u5c55\u793a\u573a\u666f\u9009\u62e9\u6781\u5750\u6807\u56fe\u6216\u5176\u4ed6\u5f62\u5f0f\u3002<\/p>\n  
    \n    
    \u793a\u4f8b\u6570\u636e\u4e2d\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u7684 Augur AUC<\/figcaption>\n    
    CellTypeC<\/span><\/span><\/span>0.879<\/span><\/div>\n    
    CellTypeB<\/span><\/span><\/span>0.747<\/span><\/div>\n    
    CellTypeA<\/span><\/span><\/span>0.554<\/span><\/div>\n    
    AUC \u8d8a\u9ad8\uff0c\u8868\u793a\u8be5\u7ec6\u80de\u7c7b\u578b\u5728\u5b9e\u9a8c\u7ec4\u4e0e\u5bf9\u7167\u7ec4\u4e4b\u95f4\u7684\u5206\u5b50\u7279\u5f81\u8d8a\u5bb9\u6613\u88ab\u6a21\u578b\u533a\u5206\u3002<\/p>\n  <\/figure>\n  
    \n    
    R \u00b7 \u63a8\u8350\u7684\u6761\u5f62\u56fe<\/span><\/div>\n    
    library<\/span>(ggplot2)\n\nauc_data <- augur_result$AUC\n\nggplot<\/span>(auc_data, aes<\/span>(x = reorder(cell_type, auc), y = auc)) +\n  geom_col<\/span>(fill = \"#2558D7\"<\/span>, width = 0.68) +\n  coord_flip<\/span>() +\n  labs<\/span>(x = NULL, y = \"Augur AUC\"<\/span>) +\n  theme_minimal<\/span>(base_size = 12)<\/code><\/pre>\n  <\/div>\n<\/section>\n\n
    \n  
    \u53c2\u6570\u4e0e\u6570\u636e\u8981\u6c42<\/h2>\n  
    \u628a Seurat \u5bf9\u8c61\u4ea4\u7ed9 Augur \u524d\uff0c\u91cd\u70b9\u68c0\u67e5\u5206\u7ec4\u5217\u3001\u7ec6\u80de\u7c7b\u578b\u5217\u548c\u8ba1\u7b97\u7ebf\u7a0b\u6570\u3002\u5b57\u6bb5\u540d\u79f0\u4e0d\u4e00\u81f4\u65f6\uff0c\u5e94\u660e\u786e\u4f20\u5165\u5bf9\u5e94\u53c2\u6570\u3002<\/p>\n  
    \n    \n      \n        
    \u9879\u76ee<\/th>\u4f5c\u7528<\/th>\u5efa\u8bae<\/th><\/tr><\/thead>\n      
    label<\/code><\/td>\u5b9e\u9a8c\u6761\u4ef6\uff0c\u5982 treatment \/ control<\/td>\u81f3\u5c11\u5305\u542b\u4e24\u4e2a\u53ef\u6bd4\u8f83\u7684\u5206\u7ec4<\/td><\/tr>\n        
    cell_type<\/code><\/td>\u7ec6\u80de\u7c7b\u578b\u6ce8\u91ca<\/td>\u5148\u68c0\u67e5\u6bcf\u7c7b\u7ec6\u80de\u6570\u91cf\u662f\u5426\u8db3\u591f<\/td><\/tr>\n        
    n_threads<\/code><\/td>\u5e76\u884c\u8ba1\u7b97\u7ebf\u7a0b\u6570<\/td>\u6839\u636e CPU \u4e0e\u5185\u5b58\u8bbe\u7f6e\uff0c\u4e0d\u662f\u8d8a\u5927\u8d8a\u597d<\/td><\/tr>\n        
    cell_type_col<\/code><\/td>\u6307\u5b9a\u7ec6\u80de\u7c7b\u578b\u5217\u540d<\/td>\u5217\u540d\u4e0d\u4e3a cell_type \u65f6\u663e\u5f0f\u4f20\u5165<\/td><\/tr>\n        
    label_col<\/code><\/td>\u6307\u5b9a\u5b9e\u9a8c\u5206\u7ec4\u5217\u540d<\/td>\u5217\u540d\u4e0d\u4e3a label \u65f6\u663e\u5f0f\u4f20\u5165<\/td><\/tr>\n      <\/tbody>\n    <\/table>\n  <\/div>\n  
    \n    
    R \u00b7 \u81ea\u5b9a\u4e49\u5b57\u6bb5\u4e0e\u7ebf\u7a0b\u6570<\/span><\/div>\n    
    augur_result <- calculate_auc<\/span>(\n  seurat_object,\n  cell_type_col = \"cell_annotation\"<\/span>,\n  label_col = \"condition\"<\/span>,\n  n_threads = 8\n)<\/code><\/pre>\n  <\/div>\n  
    \u6ce8\u610f\uff1a<\/strong>\u5c06\u7ebf\u7a0b\u6570\u4ece 4 \u8c03\u5230 8 \u4e0d\u4e00\u5b9a\u4f1a\u8ba9\u6574\u4f53\u8fd0\u884c\u65f6\u95f4\u4e25\u683c\u7f29\u77ed\u4e00\u534a\u3002\u5b9e\u9645\u901f\u5ea6\u8fd8\u53d6\u51b3\u4e8e CPU \u6838\u5fc3\u3001\u5185\u5b58\u3001\u6570\u636e\u89c4\u6a21\u548c\u5e76\u884c\u5f00\u9500\u3002<\/div>\n<\/section>\n\n
    \n  
    \u539f\u7406\u7b80\u8ff0<\/h2>\n  
    Augur \u7684\u6838\u5fc3\u601d\u8def\u662f\uff1a\u5982\u679c\u67d0\u7c7b\u7ec6\u80de\u5bf9\u5b9e\u9a8c\u523a\u6fc0\u4ea7\u751f\u4e86\u660e\u663e\u54cd\u5e94\uff0c\u90a3\u4e48\u53ea\u6839\u636e\u8be5\u7ec6\u80de\u7684\u5206\u5b50\u7279\u5f81\uff0c\u6a21\u578b\u5c31\u66f4\u5bb9\u6613\u5224\u65ad\u5b83\u6765\u81ea\u5b9e\u9a8c\u7ec4\u8fd8\u662f\u5bf9\u7167\u7ec4\u3002<\/p>\n  
    \n    
    \u6309\u7ec6\u80de\u7c7b\u578b\u62c6\u5206<\/b>\u5206\u522b\u5904\u7406\u6bcf\u4e00\u79cd\u7ec6\u80de\u7c7b\u578b\uff0c\u907f\u514d\u4e0d\u540c\u7ec6\u80de\u7fa4\u4e4b\u95f4\u7684\u5dee\u5f02\u5e72\u6270\u5224\u65ad\u3002<\/span><\/div>\n    
    \u8bad\u7ec3\u5206\u7c7b\u6a21\u578b<\/b>\u5c1d\u8bd5\u4ece\u5206\u5b50\u7279\u5f81\u9884\u6d4b\u7ec6\u80de\u6765\u81ea\u54ea\u4e00\u79cd\u5b9e\u9a8c\u6761\u4ef6\u3002<\/span><\/div>\n    
    \u4ea4\u53c9\u9a8c\u8bc1\u6392\u5e8f<\/b>\u7528 AUC \u8861\u91cf\u53ef\u5206\u6027\uff0c\u5e76\u636e\u6b64\u751f\u6210\u7ec6\u80de\u7c7b\u578b\u4f18\u5148\u7ea7\u3002<\/span><\/div>\n  <\/div>\n  
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