{"id":43156,"date":"2024-06-01T23:37:04","date_gmt":"2024-06-01T15:37:04","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43156"},"modified":"2024-06-01T23:37:07","modified_gmt":"2024-06-01T15:37:07","slug":"giotto%e5%92%8cseurat%e3%80%81spatialde-%e5%92%8c-stutility%e7%9a%84%e5%af%b9%e6%af%94","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43156","title":{"rendered":"Giotto\u548cSeurat\u3001SpatialDE \u548c STUtility\u7684\u5bf9\u6bd4"},"content":{"rendered":"\n

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

\u968f\u7740\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5b66\u6280\u672f\u7684\u53d1\u5c55\uff0c\u8d8a\u6765\u8d8a\u591a\u7684\u5de5\u5177\u548c\u8f6f\u4ef6\u5305\u88ab\u5f00\u53d1\u51fa\u6765\uff0c\u7528\u4e8e\u5904\u7406\u548c\u5206\u6790\u8fd9\u79cd\u590d\u6742\u7684\u6570\u636e\u3002\u5176\u4e2d\uff0cGiotto \u662f\u4e00\u4e2a\u65b0\u5174\u7684\u3001\u529f\u80fd\u5f3a\u5927\u7684\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5206\u6790\u5de5\u5177\uff0c\u80fd\u591f\u63d0\u4f9b\u4ece\u6570\u636e\u9884\u5904\u7406\u3001\u53ef\u89c6\u5316\u5230\u9ad8\u7ea7\u5206\u6790\u7684\u4e00\u4f53\u5316\u89e3\u51b3\u65b9\u6848\u3002\u672c\u6587\u5c06\u8be6\u7ec6\u8bb2\u89e3 Giotto\uff0c\u5e76\u5c06\u5176\u4e0e\u5176\u4ed6\u5e38\u7528\u7684\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5de5\u5177\u8fdb\u884c\u5bf9\u6bd4\uff0c\u63a2\u8ba8\u5176\u4f18\u7f3a\u70b9\u3002<\/p>\n\n\n\n

Giotto\u7b80\u4ecb<\/h4>\n\n\n\n

Giotto \u662f\u7531\u534e\u76db\u987f\u5927\u5b66\u7684\u7814\u7a76\u56e2\u961f\u5f00\u53d1\u7684\u4e00\u4e2a\u5f00\u6e90 R \u5305\uff0c\u4e13\u6ce8\u4e8e\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u7684\u53ef\u89c6\u5316\u548c\u5206\u6790\u3002Giotto \u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u529f\u80fd\uff0c\u5305\u62ec\u6570\u636e\u9884\u5904\u7406\u3001\u7a7a\u95f4\u53ef\u89c6\u5316\u3001\u805a\u7c7b\u5206\u6790\u3001\u7a7a\u95f4\u57fa\u56e0\u5171\u8868\u8fbe\u7f51\u7edc\u7b49\u3002\u4ee5\u4e0b\u662f Giotto \u7684\u4e3b\u8981\u7279\u70b9\uff1a<\/p>\n\n\n\n

    \n
  1. \u9ad8\u5ea6\u7075\u6d3b\u7684\u53ef\u89c6\u5316\u529f\u80fd<\/strong>\uff1aGiotto \u63d0\u4f9b\u4e86\u591a\u79cd\u53ef\u89c6\u5316\u9009\u9879\uff0c\u53ef\u4ee5\u751f\u6210\u9ad8\u5206\u8fa8\u7387\u7684\u4e8c\u7ef4\u548c\u4e09\u7ef4\u56fe\u50cf\u3002<\/li>\n\n\n\n
  2. \u9ad8\u7ea7\u7a7a\u95f4\u5206\u6790\u65b9\u6cd5<\/strong>\uff1a\u5305\u62ec\u7a7a\u95f4\u805a\u7c7b\u3001\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u548c\u57fa\u56e0\u5171\u8868\u8fbe\u7f51\u7edc\u5206\u6790\u3002<\/li>\n\n\n\n
  3. \u7528\u6237\u53cb\u597d<\/strong>\uff1aGiotto \u7684\u8bbe\u8ba1\u6ce8\u91cd\u7528\u6237\u4f53\u9a8c\uff0c\u63d0\u4f9b\u8be6\u7ec6\u7684\u6587\u6863\u548c\u6559\u7a0b\uff0c\u5e2e\u52a9\u7528\u6237\u5feb\u901f\u4e0a\u624b\u3002<\/li>\n<\/ol>\n\n\n\n

    Giotto\u7684\u5b89\u88c5\u548c\u57fa\u672c\u4f7f\u7528<\/h4>\n\n\n\n

    \u9996\u5148\uff0c\u5b89\u88c5\u548c\u52a0\u8f7d Giotto\uff1a<\/p>\n\n\n\n

    # \u5b89\u88c5Giotto\nif (!requireNamespace(\"remotes\", quietly = TRUE)) {\n  install.packages(\"remotes\")\n}\nremotes::install_github(\"drieslab\/Giotto\")\n\n# \u52a0\u8f7dGiotto\nlibrary(Giotto)<\/code><\/pre>\n\n\n\n
    \u6570\u636e\u5bfc\u5165\u548c\u9884\u5904\u7406<\/h4>\n\n\n\n
    \u5bfc\u5165\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u5e76\u8fdb\u884c\u9884\u5904\u7406\uff1a<\/p>\n\n\n\n
    # \u5047\u8bbe\u4f60\u6709\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u548c\u7a7a\u95f4\u5750\u6807\u6587\u4ef6\nexpr_matrix <- \"path\/to\/expression_matrix.txt\"\nspatial_coords <- \"path\/to\/spatial_coordinates.txt\"\n\n# \u521b\u5efaGiotto\u5bf9\u8c61\ngiotto_obj <- createGiottoObject(raw_exprs = expr_matrix, spatial_locs = spatial_coords)\n\n# \u6570\u636e\u5f52\u4e00\u5316\ngiotto_obj <- normalizeGiotto(gobject = giotto_obj, scalefactor = 10000)<\/code><\/pre>\n\n\n\n
    \u7a7a\u95f4\u53ef\u89c6\u5316<\/h4>\n\n\n\n
    Giotto \u63d0\u4f9b\u4e86\u5f3a\u5927\u7684\u53ef\u89c6\u5316\u529f\u80fd\uff0c\u53ef\u4ee5\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u7a7a\u95f4\u57fa\u56e0\u8868\u8fbe\u56fe\uff1a<\/p>\n\n\n\n
    # \u53ef\u89c6\u5316\u57fa\u56e0\u8868\u8fbe\nspatPlot2D(gobject = giotto_obj, genes = c(\"GeneA\", \"GeneB\"))\n\n# \u4e09\u7ef4\u53ef\u89c6\u5316\nspatPlot3D(gobject = giotto_obj, genes = c(\"GeneA\", \"GeneB\"))<\/code><\/pre>\n\n\n\n
    \u7a7a\u95f4\u805a\u7c7b\u548c\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/h4>\n\n\n\n
    Giotto \u4e5f\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u5206\u6790\u529f\u80fd\uff0c\u5982\u7a7a\u95f4\u805a\u7c7b\u548c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff1a<\/p>\n\n\n\n
    # \u7a7a\u95f4\u805a\u7c7b\ngiotto_obj <- runSpatialCluster(gobject = giotto_obj, method = \"kmeans\", k = 5)\n\n# \u5dee\u5f02\u8868\u8fbe\u5206\u6790\ndiff_expr <- findMarkers(gobject = giotto_obj, method = \"limma\")<\/code><\/pre>\n\n\n\n
    \u4e0e\u5176\u4ed6\u5de5\u5177\u7684\u5bf9\u6bd4<\/h4>\n\n\n\n
    \u5728\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u9886\u57df\uff0c\u8fd8\u6709\u8bb8\u591a\u5176\u4ed6\u5de5\u5177\uff0c\u5982 Seurat\u3001SpatialDE \u548c STUtility\u3002\u4ee5\u4e0b\u662f\u5bf9\u8fd9\u4e9b\u5de5\u5177\u7684\u5bf9\u6bd4\uff1a<\/p>\n\n\n\n
    \u529f\u80fd<\/th>Giotto<\/th>Seurat<\/th>SpatialDE<\/th>STUtility<\/th><\/tr><\/thead>
    \u6570\u636e\u9884\u5904\u7406<\/td>\u662f<\/td>\u662f<\/td>\u5426<\/td>\u662f<\/td><\/tr>
    \u7a7a\u95f4\u53ef\u89c6\u5316<\/td>2D \u548c 3D \u53ef\u89c6\u5316<\/td>\u4e3b\u8981\u4e3a 2D \u53ef\u89c6\u5316<\/td>\u5426<\/td>\u4e3b\u8981\u4e3a 2D \u53ef\u89c6\u5316<\/td><\/tr>
    \u7a7a\u95f4\u805a\u7c7b<\/td>\u662f<\/td>\u662f<\/td>\u662f<\/td>\u662f<\/td><\/tr>
    \u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/td>\u662f<\/td>\u662f<\/td>\u662f<\/td>\u662f<\/td><\/tr>
    \u9ad8\u7ea7\u5206\u6790\u529f\u80fd<\/td>\u7a7a\u95f4\u57fa\u56e0\u5171\u8868\u8fbe\u7f51\u7edc\uff0c\u4e09\u7ef4\u53ef\u89c6\u5316<\/td>\u4e30\u5bcc\u7684\u5355\u7ec6\u80de\u5206\u6790\u529f\u80fd<\/td>\u4e3b\u8981\u4e3a\u7a7a\u95f4\u5dee\u5f02\u8868\u8fbe\u68c0\u6d4b<\/td>\u4e13\u6ce8\u4e8e\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u7684\u57fa\u672c\u5206\u6790<\/td><\/tr>
    \u7528\u6237\u53cb\u597d\u6027<\/td>\u9ad8<\/td>\u9ad8<\/td>\u4e2d<\/td>\u9ad8<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n
    Giotto\u7684\u4f18\u7f3a\u70b9<\/h4>\n\n\n\n
    \u4f18\u70b9\uff1a<\/strong><\/p>\n\n\n\n
      \n
    1. \u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u529f\u80fd<\/strong>\uff1aGiotto \u63d0\u4f9b\u4e862D\u548c3D\u7684\u53ef\u89c6\u5316\u9009\u9879\uff0c\u53ef\u4ee5\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u56fe\u50cf\uff0c\u5e2e\u52a9\u7528\u6237\u6df1\u5165\u7406\u89e3\u6570\u636e\u3002<\/li>\n\n\n\n
    2. \u9ad8\u7ea7\u7a7a\u95f4\u5206\u6790<\/strong>\uff1a\u5305\u62ec\u7a7a\u95f4\u57fa\u56e0\u5171\u8868\u8fbe\u7f51\u7edc\u5206\u6790\u548c\u9ad8\u7ea7\u805a\u7c7b\u65b9\u6cd5\uff0c\u4e3a\u7528\u6237\u63d0\u4f9b\u4e86\u5f3a\u5927\u7684\u5206\u6790\u5de5\u5177\u3002<\/li>\n\n\n\n
    3. \u7528\u6237\u53cb\u597d<\/strong>\uff1a\u8be6\u7ec6\u7684\u6587\u6863\u548c\u6559\u7a0b\uff0c\u4f7f\u5f97\u65b0\u624b\u4e5f\u80fd\u5feb\u901f\u4e0a\u624b\u3002<\/li>\n<\/ol>\n\n\n\n
      \u7f3a\u70b9\uff1a<\/strong><\/p>\n\n\n\n
        \n
      1. \u8ba1\u7b97\u8d44\u6e90\u9700\u6c42\u8f83\u9ad8<\/strong>\uff1a\u7531\u4e8e\u5176\u4e30\u5bcc\u7684\u529f\u80fd\u548c\u9ad8\u7ea7\u5206\u6790\u65b9\u6cd5\uff0cGiotto \u5bf9\u8ba1\u7b97\u8d44\u6e90\u7684\u9700\u6c42\u8f83\u9ad8\uff0c\u53ef\u80fd\u5bf9\u786c\u4ef6\u8981\u6c42\u8f83\u9ad8\u3002<\/li>\n\n\n\n
      2. \u5b66\u4e60\u66f2\u7ebf\u8f83\u9661<\/strong>\uff1a\u867d\u7136 Giotto \u63d0\u4f9b\u4e86\u8be6\u7ec6\u7684\u6587\u6863\uff0c\u4f46\u7531\u4e8e\u5176\u529f\u80fd\u4e30\u5bcc\uff0c\u7528\u6237\u53ef\u80fd\u9700\u8981\u82b1\u8d39\u4e00\u5b9a\u65f6\u95f4\u6765\u719f\u6089\u548c\u638c\u63e1\u6240\u6709\u529f\u80fd\u3002<\/li>\n<\/ol>\n\n\n\n
        \u7ed3\u8bba<\/h4>\n\n\n\n
        Giotto \u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u4e14\u7075\u6d3b\u7684\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u5de5\u5177\uff0c\u7279\u522b\u9002\u5408\u9700\u8981\u9ad8\u7ea7\u5206\u6790\u548c\u9ad8\u8d28\u91cf\u53ef\u89c6\u5316\u7684\u7528\u6237\u3002\u867d\u7136\u5176\u5b66\u4e60\u66f2\u7ebf\u8f83\u9661\uff0c\u4f46\u901a\u8fc7\u8be6\u7ec6\u7684\u6587\u6863\u548c\u6559\u7a0b\uff0c\u7528\u6237\u53ef\u4ee5\u9010\u6b65\u638c\u63e1\u5176\u4e30\u5bcc\u7684\u529f\u80fd\u3002\u4e0e\u5176\u4ed6\u5de5\u5177\u76f8\u6bd4\uff0cGiotto \u5728\u53ef\u89c6\u5316\u548c\u9ad8\u7ea7\u5206\u6790\u65b9\u9762\u5177\u6709\u663e\u8457\u4f18\u52bf\uff0c\u4f46\u4e5f\u9700\u8981\u66f4\u591a\u7684\u8ba1\u7b97\u8d44\u6e90\u3002<\/p>\n\n\n\n
        \u5e0c\u671b\u8fd9\u7bc7\u6587\u7ae0\u80fd\u5e2e\u52a9\u4f60\u66f4\u597d\u5730\u7406\u89e3 Giotto \u53ca\u5176\u5728\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u4e2d\u7684\u5e94\u7528\u3002\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":"
        \u968f\u7740\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u5b66\u6280\u672f\u7684\u53d1\u5c55\uff0c\u8d8a\u6765\u8d8a\u591a\u7684\u5de5\u5177\u548c\u8f6f\u4ef6\u5305\u88ab\u5f00\u53d1\u51fa\u6765\uff0c\u7528\u4e8e\u5904\u7406\u548c\u5206\u6790\u8fd9\u79cd\u590d\u6742\u7684\u6570\u636e\u3002\u5176\u4e2d\uff0cGiotto […]<\/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\/43156"}],"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=43156"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/43156\/revisions"}],"predecessor-version":[{"id":43157,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/43156\/revisions\/43157"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=43156"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=43156"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=43156"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}