{"id":43154,"date":"2024-06-01T23:35:17","date_gmt":"2024-06-01T15:35:17","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43154"},"modified":"2024-06-01T23:35:19","modified_gmt":"2024-06-01T15:35:19","slug":"stutility-%e8%af%a6%e7%bb%86%e8%ae%b2%e8%a7%a3%e5%8f%8a%e7%a4%ba%e4%be%8b","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43154","title":{"rendered":"STUtility \u8be6\u7ec6\u8bb2\u89e3\u53ca\u793a\u4f8b"},"content":{"rendered":"\n

<\/h3>\n\n\n\n

STUtility \u662f\u4e00\u4e2a\u57fa\u4e8e R \u7684\u5305\uff0c\u4e13\u4e3a\u5206\u6790\u548c\u53ef\u89c6\u5316\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u800c\u8bbe\u8ba1\u3002\u5b83\u63d0\u4f9b\u4e86\u4ece\u6570\u636e\u9884\u5904\u7406\u3001\u5f52\u4e00\u5316\u3001\u805a\u7c7b\u5230\u53ef\u89c6\u5316\u7684\u4e00\u6574\u5957\u89e3\u51b3\u65b9\u6848\u3002\u4ee5\u4e0b\u662f\u5173\u4e8e STUtility \u7684\u8be6\u7ec6\u8bb2\u89e3\uff0c\u5305\u62ec\u4e00\u4e9b\u57fa\u672c\u529f\u80fd\u7684\u793a\u4f8b\u548c\u4ee3\u7801\u3002<\/p>\n\n\n\n

\u5b89\u88c5\u548c\u52a0\u8f7d STUtility<\/h4>\n\n\n\n

\u9996\u5148\uff0c\u9700\u8981\u5728 R \u73af\u5883\u4e2d\u5b89\u88c5\u5e76\u52a0\u8f7d STUtility \u5305\uff1a<\/p>\n\n\n\n

# \u5b89\u88c5 STUtility \u5305\nif (!requireNamespace(\"remotes\", quietly = TRUE)) {\n  install.packages(\"remotes\")\n}\nremotes::install_github(\"jbergenstrahle\/STUtility\")\n\n# \u52a0\u8f7d STUtility \u5305\nlibrary(STUtility)<\/code><\/pre>\n\n\n\n
\u6570\u636e\u5bfc\u5165\u4e0e\u9884\u5904\u7406<\/h4>\n\n\n\n
\u5047\u8bbe\u4f60\u5df2\u7ecf\u6709\u4e86\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u7684\u539f\u59cb\u6570\u636e\uff0c\u53ef\u4ee5\u901a\u8fc7 InputFromTable<\/code> \u51fd\u6570\u5bfc\u5165\u6570\u636e\u3002\u4ee5\u4e0b\u662f\u4e00\u4e2a\u793a\u4f8b\uff1a<\/p>\n\n\n\n
# \u8bbe\u5b9a\u6587\u4ef6\u8def\u5f84\ndata_dir <- \"path\/to\/your\/data\"\n\n# \u5bfc\u5165\u6570\u636e\nst_data <- InputFromTable(data_path = data_dir, sep = \"\\t\")\n\n# \u67e5\u770b\u6570\u636e\u6982\u89c8\nprint(st_data)<\/code><\/pre>\n\n\n\n
\u6570\u636e\u5f52\u4e00\u5316<\/h4>\n\n\n\n
\u4e3a\u4e86\u6d88\u9664\u6280\u672f\u566a\u97f3\u548c\u6d4b\u5e8f\u6df1\u5ea6\u7684\u5dee\u5f02\uff0c\u6570\u636e\u5f52\u4e00\u5316\u662f\u5fc5\u8981\u7684\u3002STUtility \u63d0\u4f9b\u4e86\u591a\u79cd\u5f52\u4e00\u5316\u65b9\u6cd5\uff1a<\/p>\n\n\n\n
# \u5f52\u4e00\u5316\u6570\u636e\nst_data <- NormalizeData(object = st_data, normalization.method = \"LogNormalize\", scale.factor = 10000)<\/code><\/pre>\n\n\n\n
\u7a7a\u95f4\u53ef\u89c6\u5316<\/h4>\n\n\n\n
STUtility \u53ef\u4ee5\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u6620\u5c04\u5230\u7ec4\u7ec7\u5207\u7247\u7684\u7a7a\u95f4\u5750\u6807\u4e0a\uff0c\u5e76\u8fdb\u884c\u53ef\u89c6\u5316\uff1a<\/p>\n\n\n\n
# \u53ef\u89c6\u5316\u7279\u5b9a\u57fa\u56e0\u7684\u7a7a\u95f4\u8868\u8fbe\u6a21\u5f0f\nSpatialFeaturePlot(object = st_data, features = c(\"GeneA\", \"GeneB\"))<\/code><\/pre>\n\n\n\n
\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/h4>\n\n\n\n
STUtility \u63d0\u4f9b\u4e86\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7684\u529f\u80fd\uff0c\u53ef\u4ee5\u7528\u4e8e\u8bc6\u522b\u5728\u4e0d\u540c\u7a7a\u95f4\u4f4d\u7f6e\u4e0a\u663e\u8457\u8868\u8fbe\u7684\u57fa\u56e0\uff1a<\/p>\n\n\n\n
# \u627e\u51fa\u7279\u5b9a\u533a\u57df\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\nmarkers <- FindMarkers(object = st_data, ident.1 = \"Region1\", ident.2 = \"Region2\", min.pct = 0.25)\nprint(markers)<\/code><\/pre>\n\n\n\n
\u7a7a\u95f4\u805a\u7c7b\u5206\u6790<\/h4>\n\n\n\n
\u901a\u8fc7\u805a\u7c7b\u5206\u6790\uff0c\u53ef\u4ee5\u8bc6\u522b\u51fa\u529f\u80fd\u4e0a\u6216\u7ed3\u6784\u4e0a\u76f8\u4f3c\u7684\u7ec6\u80de\u7fa4\u4f53\uff1a<\/p>\n\n\n\n
# \u8fd0\u884c\u805a\u7c7b\u5206\u6790\nst_data <- FindClusters(object = st_data, resolution = 0.5)\n\n# \u53ef\u89c6\u5316\u805a\u7c7b\u7ed3\u679c\nSpatialDimPlot(object = st_data)<\/code><\/pre>\n\n\n\n
\u5b8c\u6574\u793a\u4f8b<\/h4>\n\n\n\n
\u4ee5\u4e0b\u662f\u4e00\u4e2a\u5b8c\u6574\u7684\u793a\u4f8b\uff0c\u5c55\u793a\u4e86\u4ece\u6570\u636e\u5bfc\u5165\u5230\u53ef\u89c6\u5316\u7684\u6574\u4e2a\u6d41\u7a0b\uff1a<\/p>\n\n\n\n
# \u5b89\u88c5\u548c\u52a0\u8f7d\u5fc5\u8981\u7684\u5305\nif (!requireNamespace(\"remotes\", quietly = TRUE)) {\n  install.packages(\"remotes\")\n}\nremotes::install_github(\"jbergenstrahle\/STUtility\")\nlibrary(STUtility)\n\n# \u6570\u636e\u5bfc\u5165\ndata_dir <- \"path\/to\/your\/data\"\nst_data <- InputFromTable(data_path = data_dir, sep = \"\\t\")\n\n# \u6570\u636e\u9884\u5904\u7406\nst_data <- NormalizeData(object = st_data, normalization.method = \"LogNormalize\", scale.factor = 10000)\n\n# \u7a7a\u95f4\u53ef\u89c6\u5316\nSpatialFeaturePlot(object = st_data, features = c(\"GeneA\", \"GeneB\"))\n\n# \u5dee\u5f02\u8868\u8fbe\u5206\u6790\nmarkers <- FindMarkers(object = st_data, ident.1 = \"Region1\", ident.2 = \"Region2\", min.pct = 0.25)\nprint(markers)\n\n# \u7a7a\u95f4\u805a\u7c7b\u5206\u6790\nst_data <- FindClusters(object = st_data, resolution = 0.5)\nSpatialDimPlot(object = st_data)<\/code><\/pre>\n\n\n\n
\u7ed3\u8bba<\/h4>\n\n\n\n
STUtility \u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u7684\u5de5\u5177\u5305\uff0c\u9002\u7528\u4e8e\u5904\u7406\u548c\u5206\u6790\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u3002\u901a\u8fc7\u672c\u6587\u7684\u8bb2\u89e3\u548c\u793a\u4f8b\u4ee3\u7801\uff0c\u4f60\u5e94\u8be5\u80fd\u591f\u638c\u63e1\u5176\u57fa\u672c\u529f\u80fd\u548c\u4f7f\u7528\u65b9\u6cd5\u3002\u968f\u7740\u4f60\u5bf9\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5b66\u7684\u6df1\u5165\u4e86\u89e3\uff0c\u4f60\u53ef\u4ee5\u5229\u7528 STUtility \u8fdb\u884c\u66f4\u52a0\u590d\u6742\u548c\u8be6\u7ec6\u7684\u6570\u636e\u5206\u6790\uff0c\u4e3a\u4f60\u7684\u7814\u7a76\u63d0\u4f9b\u6709\u529b\u7684\u652f\u6301\u3002<\/p>\n\n\n\n
\u5e0c\u671b\u8fd9\u7bc7\u535a\u5ba2\u6587\u7ae0\u5bf9\u4f60\u6709\u6240\u5e2e\u52a9\uff0c\u5982\u679c\u6709\u4efb\u4f55\u95ee\u9898\u6216\u9700\u8981\u8fdb\u4e00\u6b65\u7684\u6307\u5bfc\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
STUtility \u662f\u4e00\u4e2a\u57fa\u4e8e R \u7684\u5305\uff0c\u4e13\u4e3a\u5206\u6790\u548c\u53ef\u89c6\u5316\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u800c\u8bbe\u8ba1\u3002\u5b83\u63d0\u4f9b\u4e86\u4ece\u6570\u636e\u9884\u5904\u7406\u3001\u5f52\u4e00\u5316\u3001 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/43154"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=43154"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/43154\/revisions"}],"predecessor-version":[{"id":43155,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/43154\/revisions\/43155"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=43154"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=43154"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=43154"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}