{"id":29222,"date":"2024-02-21T17:46:23","date_gmt":"2024-02-21T09:46:23","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29222"},"modified":"2024-02-21T17:46:24","modified_gmt":"2024-02-21T09:46:24","slug":"%e4%b8%80%e6%96%87%e5%ad%a6%e4%bc%9a%e5%88%a9%e7%94%a8scmetabolism-%e5%8c%85%e8%bf%9b%e8%a1%8c%e5%8d%95%e7%bb%86%e8%83%9e%e4%bb%a3%e8%b0%a2%e6%b4%bb%e6%80%a7%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29222","title":{"rendered":"\u4e00\u6587\u5b66\u4f1a\u5229\u7528scMetabolism \u5305\u8fdb\u884c\u5355\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027\u5206\u6790"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u60f3\u5e26\u7740\u5c0f\u4f19\u4f34\u4e00\u8d77\u5b66\u4e60\u5982\u4f55\u5229\u7528scMetabolism R\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027\u7684\u5206\u6790\uff0c\u8be5\u5305\u53ef\u4ee5\u5bf9\u6bcf\u4e00\u4e2a\u7ec6\u80de\u7c7b\u578b\u8fdb\u884c\u8fdb\u884c\u4ee3\u8c22\u6d3b\u6027\u7684\u63a8\u65ad\uff0c\u4f7f\u7528\u7684\u4ee3\u8c22\u6570\u636e\u96c6\u6765\u81eaKEGG\u548cREACTOME\u4e24\u4e2a\u6570\u636e\u5e93\uff0c\u5305\u542b4\u79cd\u7b97\u6cd5\u53ef\u4ee5\u8fdb\u884c\u9009\u62e9\uff0cssGSEA,AUCell,VISION\u548cGSVA\uff0c\u6700\u540e\u53ef\u4ee5\u7ed8\u5236\u6c14\u6ce1\u56fe\uff0cumap\u56fe\u548c\u7bb1\u7ebf\u56fe\u6765\u5c55\u793a\u4e0d\u540c\u7c7b\u578b\u7ec6\u80de\u7684\u4ee3\u8c22\u6d3b\u6027\uff0c\u60f3\u6df1\u5165\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u53c2\u8003\u7f51\u7ad9\uff1ahttps:\/\/github.com\/wu-yc\/scMetabolism\uff0c\u8bdd\u4e0d\u591a\u8bf4\uff0c\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

    install.packages(“devtools”)<\/p>\n

    install.packages(“data.table”)<\/p>\n

    install.packages(“wesanderson”)<\/p>\n

    install.packages(\u201cAUCell\u201d)<\/p>\n

    install.packages(\u201cGSEABase\u201d)<\/p>\n

    install.packages(\u201cGSVA\u201d)<\/p>\n

    install.packages(\u201cggplot2\u201d)<\/p>\n

    install.packages(\u201crsvd\u201d)<\/p>\n

    devtools::install_github(“YosefLab\/VISION”)<\/p>\n

    devtools::install_github(“wu-yc\/scMetabolism”)<\/p>\n

      \n
    1. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(phangorn)<\/p>\n

      library(scMetabolism)<\/p>\n

      library(ggplot2)<\/p>\n

      library(rsvd)<\/p>\n

      library(AUCell)<\/p>\n

      library(GSEABase)<\/p>\n

      library(GSVA)<\/p>\n

        \n
      1. \u793a\u4f8b\u6570\u636e<\/li>\n<\/ol>\n

        load(file = “pbmc_demo.rda”)<\/p>\n

        4.\u4ee3\u7801\u5c55\u793a<\/p>\n

        #\u901a\u8fc7AUCell\u7b97\u6cd5\u6765\u8ba1\u7b97\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027(\u6b64\u5904\u5f00\u59cb\u6536\u8d39)<\/p>\n

        countexp.Seurat<-sc.metabolism.Seurat(obj = countexp.Seurat, method = “AUCell”, imputation =F, ncores = 2, metabolism.type = “KEGG”)<\/p>\n

        #obj\u8868\u793a\u5355\u7ec6\u80deseurat\u5206\u6790\u7ed3\u679c\u6570\u636e<\/p>\n

        #metho\u8868\u793a\u901a\u8fc7\u54ea\u79cd\u7b97\u6cd5\u8fdb\u884c\u8ba1\u7b97<\/p>\n

        #ncores\u8868\u793a\u7ebf\u7a0b\u6570<\/p>\n

        #metabolism.type\u8868\u793a\u9009\u62e9\u7684\u4ee3\u8c22\u6570\u636e\u5e93\u7c7b\u578b\uff0c\u5176\u4e2dKEGG\u6570\u636e\u5e93\u5305\u542b85\u6761\u4ee3\u8c22\u9014\u5f84\uff0cREACTOME\u6570\u636e\u5e93\u5305\u542b82\u6761\u4ee3\u8c22\u9014\u5f84\u3002<\/p>\n

        #\u5982\u679c\u60f3\u63d0\u53d6metabolism score\uff0c\u53ef\u4ee5\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\u3002<\/p>\n

        metabolism.matrix <- countexp.Seurat@assays$METABOLISM$score<\/p>\n

        metabolism.matrix \u6570\u636e\u7c7b\u578b\u4e3a\u4e00\u4e2a\u77e9\u9635\u3002<\/p>\n

        \"Dingtalk_20230324213919\"<\/p>\n

        #\u901a\u8fc7umap\u65b9\u5f0f\u5c55\u793a\u7279\u5b9a\u901a\u8def\u7684\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027<\/p>\n

        DimPlot.metabolism(obj = countexp.Seurat, pathway = “Glycolysis \/ Gluconeogenesis”, dimention.reduction.type = “umap”, dimention.reduction.run = F, size = 1)<\/p>\n

        \"Dingtalk_20230324211612\"<\/p>\n

        \u6ce8\uff1a\u8be5\u56fe\u7247\u901a\u8fc7umap\u7684\u65b9\u5f0f\u5c55\u793a\u4e86\u7279\u5b9a\u4ee3\u8c22\u901a\u8def\u7ec6\u80de\u7684\u4ee3\u8c22\u6d3b\u6027\uff0c\u901a\u8fc7\u4e0d\u540c\u989c\u8272\u6765\u8868\u793a\u4ee3\u8c22\u6d3b\u6027\u7684\u9ad8\u4f4e\u3002<\/p>\n

        #\u901a\u8fc7\u6c14\u6ce1\u56fe\u7684\u65b9\u5f0f\u5c55\u793a\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027<\/p>\n

        input.pathway<-c(“Glycolysis \/ Gluconeogenesis”, “Oxidative phosphorylation”, “Citrate cycle (TCA cycle)”)<\/p>\n

        DotPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = “ident”, norm = “y”)<\/p>\n

        \"Dingtalk_20230324211804\"<\/p>\n

        \u6ce8\uff1a\u8be5\u56fe\u8868\u793a\u4e0d\u540c\u7ec6\u80de\u7684\u6d3b\u6027\u7684\u4ee3\u8c22\u6d3b\u6027\uff0c\u6a2a\u5750\u6807\u8868\u793a\u7ec6\u80de\u7c7b\u578b\uff0c\u7eb5\u5750\u6807\u8868\u793a\u4ee3\u8c22\u9014\u5f84\uff0c\u989c\u8272\u4ee3\u8868value\u503c\uff0c\u989c\u8272\u8d8a\u6df1\u8868\u793a\u6d3b\u6027\u8d8a\u9ad8\u3002<\/p>\n

        #\u901a\u8fc7\u7bb1\u7ebf\u56fe\u7684\u65b9\u5f0f\u5c55\u793a\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027<\/p>\n

        BoxPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = “ident”, ncol = 1)<\/p>\n

        \"Dingtalk_20230324211341\"<\/p>\n

        \u6ce8\uff1a\u8be5\u56fe\u901a\u8fc7\u5206\u9762\u7bb1\u7ebf\u56fe\u6765\u5c55\u793a\u4e0d\u540c\u4ee3\u8c22\u901a\u8def\u7ec6\u80de\u7684\u4ee3\u8c22\u6d3b\u6027\uff0c\u7eb5\u5750\u6807\u8868\u793a\u7ec6\u80de\u6d3b\u6027\u9ad8\u4f4e\uff0c\u6a2a\u5750\u6807\u8868\u793a\u7ec6\u80de\u7c7b\u578b\u3002<\/p>\n

        #\u5982\u679c\u6570\u636e\u53ea\u6709UMI count ,\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u8fdb\u884c\u5206\u6790\uff0c\u9700\u8981\u6ce8\u610f\u7684\u662f\u6570\u636e\u7c7b\u578b\u4e3a\u5217\u4e3a\u7ec6\u80deID\uff0c\u884c\u4e3a\u57fa\u56e0name\u3002<\/p>\n

        metabolism.matrix<-sc.metabolism(countexp = countexp, method = “AUCell”, imputation = F, ncores = 2, metabolism.type = “KEGG”)<\/p>\n

        \u6700\u7ec8\u5c0f\u679c\u987a\u5229\u7684\u5b8c\u6210\u4e86\u5355\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027\u5206\u6790\uff0c\u6574\u4e2a\u5206\u6790\u8fc7\u7a0b\u8fd8\u662f\u5f88easy\u7684\uff0c\u5c0f\u4f19\u4f34\u4eec\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u5965\uff0c\u5728\u505a\u8be5\u5206\u6790\u65f6\u8fd8\u662f\u9700\u8981\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u8981\u719f\u7ec3\u638c\u63e1\uff0c\u5982\u679c\u5c0f\u4f19\u4f34\u9700\u8981\u8fdb\u884c\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\uff0c\u63a8\u8350\u5927\u5bb6\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff0c\u5305\u542b\u5355\u7ec6\u80de\u5206\u6790(http:\/\/www.biocloudservice.com\/366\/366.php)\uff0c\u7ed8\u5236\u5355\u7ec6\u80detSNE\u56fe(http:\/\/www.biocloudservice.com\/229\/229.php)\uff0c\u5355\u7ec6\u80de\u6570\u636e\u7ed8\u5236\u5c0f\u7434\u56fe(http:\/\/www.biocloudservice.com\/788\/788.php)\u7b49\u5c0f\u5de5\u5177,\u5c0f\u679c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u5965\uff0c\u4e0b\u671f\u518d\u89c1\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u60f3\u5e26\u7740\u5c0f\u4f19\u4f34\u4e00\u8d77\u5b66\u4e60\u5982\u4f55\u5229\u7528scMetabolism R\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u4ee3\u8c22\u6d3b\u6027\u7684\u5206\u6790\uff0c\u8be5\u5305\u53ef\u4ee5\u5bf9\u6bcf\u4e00\u4e2a\u7ec6 […]<\/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\/29222"}],"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=29222"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29222\/revisions"}],"predecessor-version":[{"id":29227,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29222\/revisions\/29227"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29222"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29222"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29222"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}