{"id":61531,"date":"2024-10-30T15:35:43","date_gmt":"2024-10-30T07:35:43","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61531"},"modified":"2024-10-30T15:35:43","modified_gmt":"2024-10-30T07:35:43","slug":"%e6%8e%a2%e7%b4%a2%e8%bf%9b%e5%8c%96%e5%85%b3%e7%b3%bb%e4%b9%8b%e8%bf%9b%e5%8c%96%e6%a0%91%e7%bb%98%e5%88%b6%e6%96%b0%e7%af%87%e7%ab%a0%ef%bc%9aggtree%e4%b8%8eape%e5%8c%85%e7%9a%84%e7%bb%93%e5%90%88","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61531","title":{"rendered":"\u63a2\u7d22\u8fdb\u5316\u5173\u7cfb\u4e4b\u8fdb\u5316\u6811\u7ed8\u5236\u65b0\u7bc7\u7ae0\uff1aggtree\u4e0eape\u5305\u7684\u7ed3\u5408\uff01\u5305\u4f60\u8f7b\u677e\u638c\u63e1\u751f\u7269\u8fdb\u5316\u53ef\u89c6\u5316\uff01"},"content":{"rendered":"\n

<\/p>\n\n\n\n

\u5927\u5bb6\u597d~\u6211\u662f\u5c0f\u679c!\u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u662f\u5426\u548c\u5c0f\u679c\u4e00\u6837\u5bf9\u751f\u7269\u7684\u8d77\u6e90\u548c\u53d1\u5c55\u597d\u5947\u5462\uff1f\u5b83\u4eec\u662f\u5982\u4f55\u4ece\u8fdc\u53e4\u65f6\u671f\u6f14\u5316\u81f3\u4eca\uff0c\u5f62\u6210\u4e86\u4eca\u5929\u6211\u4eec\u6240\u89c1\u5230\u7684\u5f62\u6001\u5404\u5f02\u3001\u529f\u80fd\u72ec\u7279\u7684\u751f\u7269\u79cd\u7c7b\uff1f\u4eca\u5929\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u63a2\u7d22\u8fd9\u4ebf\u4e07\u5e74\u7684\u751f\u7269\u6f14\u53d8\u5386\u7a0b\uff0c\u63ed\u5f00\u751f\u7269\u8fdb\u5316\u7684\u795e\u79d8\u9762\u7eb1\u3002\u5c0f\u679c\u672c\u671f\u5c06\u4f7f\u7528ggtree\u548cape\u8fd9\u4e24\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u5b83\u4eec\u4e0d\u4ec5\u80fd\u591f\u7ed8\u5236\u51fa\u4ee4\u4eba\u60ca\u53f9\u7684\u751f\u7269\u8fdb\u5316\u6811\uff0c\u8fd8\u80fd\u5e2e\u52a9\u6211\u4eec\u6df1\u5165\u7406\u89e3\u751f\u7269\u95f4\u7684\u4eb2\u7f18\u5173\u7cfb\u548c\u6f14\u5316\u8def\u5f84\u3002\u4e0d\u8bba\u4f60\u662f\u5bf9\u751f\u7269\u4fe1\u606f\u5b66\u5145\u6ee1\u70ed\u60c5\u7684\u65b0\u624b\uff0c\u8fd8\u662f\u5df2\u7ecf\u5728\u8fd9\u4e2a\u9886\u57df\u6709\u7740\u4e30\u5bcc\u7ecf\u9a8c\u7684\u4e13\u5bb6\uff0c\u90fd\u4e0d\u8981\u9519\u8fc7\u8fd9\u6b21\u6df1\u5165\u4e86\u89e3\u751f\u547d\u5965\u79d8\u7684\u673a\u4f1a\u3002\u8ba9\u6211\u4eec\u7528ggtree\u548cape\u8fd9\u4e24\u4e2a\u5de5\u5177\uff0c\u5f00\u542f\u63a2\u7d22\u751f\u7269\u8fdb\u5316\u7684\u5927\u95e8\uff0c\u4f53\u9a8c\u4ebf\u4e07\u5e74\u95f4\u751f\u7269\u6f14\u53d8\u7684\u58ee\u4e3d\u53f2\u8bd7\uff0c\u5171\u540c\u611f\u53d7\u751f\u547d\u4e4b\u6811\u7684\u65e0\u9650\u9b45\u529b\uff01\u5feb\u548c\u5c0f\u679c\u4e00\u8d77\u8e0f\u4e0a\u8fd9\u573a\u6fc0\u52a8\u4eba\u5fc3\u7684\u63a2\u7d22\u4e4b\u65c5\uff0c\u53d1\u73b0\u751f\u547d\u7684\u65e0\u9650\u53ef\u80fd\uff0c\u9886\u7565\u81ea\u7136\u754c\u7684\u5947\u5999\u548c\u4f1f\u5927\uff01\u540c\u65f6\u5462\uff0c\u5341\u5e74\u7684\u751f\u4fe1\u4e4b\u8def\uff0c\u5c0f\u679c\u5df2\u7ecf\u7ec3\u5c31\u4e86\u4e00\u8eab\u624e\u5b9e\u7684\u672c\u9886\uff0c\u73b0\u5728\u51c6\u5907\u7528\u8fd9\u8eab\u672c\u4e8b\u4e3a\u5c0f\u4f19\u4f34\u4eec\u670d\u52a1\u5566\uff01\u5982\u679c\u4f60\u5728\u751f\u4fe1\u5206\u6790\u4e0a\u9047\u5230\u4e86\u96be\u9898\uff0c\u90a3\u5c31\u6765\u627e\u5c0f\u679c\u5427\uff01\u5c0f\u679c\u4f1a\u7528\u81ea\u5df1\u7684\u4e13\u4e1a\u77e5\u8bc6\u548c\u6280\u80fd\uff0c\u4e3a\u4f60\u89e3\u51b3\u56f0\u6270\uff0c\u52a9\u4f60\u4e00\u81c2\u4e4b\u529b\u3002\u671f\u5f85\u4f60\u7684\u8054\u7cfb\u54e6~<\/strong><\/p>\n\n\n\n

\u4e00\u3001 <\/strong>ggtree\u4e0eape R<\/strong>\u5305\u7b80\u8981\u4ecb\u7ecd<\/strong><\/strong><\/h3>\n\n\n\n
    \n
  • ggtree R\u5305\u4ecb\u7ecd<\/em><\/strong><\/em><\/strong><\/em><\/strong><\/em><\/strong><\/li>\n<\/ul>\n\n\n\n

    ggtree\u662fggplot2\u7684\u62d3\u5c55\u5305\uff0c\u4e13\u95e8\u7528\u4e8e\u7ed8\u5236\u751f\u7269\u8fdb\u5316\u6811\u5e76\u8fdb\u884c\u4e30\u5bcc\u7684\u6ce8\u91ca\u5206\u6790\u3002\u8fd9\u4e00\u5de5\u5177\u7531\u9999\u6e2f\u5927\u5b66\u4f59\u5149\u521b\u535a\u58eb\u7f16\u5199\uff0c\u65e8\u5728\u901a\u8fc7\u56fe\u5c42\u5316\u7684\u8bed\u6cd5\u6765\u7ed8\u5236\u590d\u6742\u7684\u8fdb\u5316\u6811\u56fe\u5f62\u3002\u4e0eggplot2\u7c7b\u4f3c\uff0cggtree\u5141\u8bb8\u7528\u6237\u901a\u8fc7\u7ec4\u5408\u4e0d\u540c\u7684\u56fe\u5c42\u6765\u521b\u5efa\u9ad8\u5ea6\u5b9a\u5236\u5316\u7684\u56fe\u5f62\u3002<\/p>\n\n\n\n

      \n
    • \u6838\u5fc3\u529f\u80fd\u53ca\u7279\u70b9\uff1a<\/em><\/strong><\/em><\/strong><\/em><\/strong><\/em><\/strong><\/li>\n\n\n\n
    • \u5e7f\u6cdb\u7684\u6587\u4ef6\u683c\u5f0f\u652f\u6301\uff1aggtree\u80fd\u591f\u8bfb\u53d6\u5e76\u8f6c\u6362\u591a\u79cd\u8f6f\u4ef6\uff08\u5982BEAST\u3001r8s\u3001RAxML\u7b49\uff09\u6240\u751f\u6210\u7684\u6570\u636e\u683c\u5f0f\uff0c\u5305\u62ecNewick\u3001Nexus\u7b49\u3002<\/li>\n\n\n\n
    • \u4e30\u5bcc\u7684\u6ce8\u91ca\u529f\u80fd\uff1a\u9664\u4e86\u57fa\u672c\u7684\u8fdb\u5316\u6811\u7ed8\u5236\u5916\uff0cggtree\u8fd8\u652f\u6301\u5728\u6811\u4e0a\u6dfb\u52a0\u4e30\u5bcc\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u5982\u8282\u70b9\u6807\u7b7e\u3001\u5206\u652f\u957f\u5ea6\u3001\u7269\u79cd\u540d\u79f0\u7b49\u3002<\/li>\n\n\n\n
    • \u9ad8\u5ea6\u7684\u7075\u6d3b\u6027\uff1a\u7528\u6237\u53ef\u4ee5\u901a\u8fc7\u8c03\u6574\u53c2\u6570\u6765\u5b9a\u5236\u56fe\u5f62\u7684\u5916\u89c2\u548c\u5e03\u5c40\uff0c\u5982\u6811\u72b6\u56fe\u7684\u5f62\u72b6\uff08\u77e9\u5f62\u3001\u6247\u5f62\u7b49\uff09\u3001\u5f00\u653e\u89d2\u5ea6\u7b49\u3002<\/li>\n<\/ul>\n\n\n\n

      ggtree\u81ea\u53d1\u5e03\u4ee5\u6765\u53d7\u5230\u4e86\u56fd\u9645\u540c\u884c\u7684\u5e7f\u6cdb\u8d5e\u8a89\u3002\u76f8\u5173\u8bba\u6587\u5728\u82f1\u56fd\u751f\u6001\u5b66\u4f1a\u7684Methods in Ecology and Evolution\u53d1\u8868\u540e\uff0c\u5728\u4e0d\u5230\u4e00\u5e74\u7684\u65f6\u95f4\u91cc\u5f15\u7528\u6b21\u6570\u5df2\u7ecf\u8d85\u8fc7100\u6b21\uff0c\u663e\u793a\u51fa ggtree R\u5305\u53d7\u6b22\u8fce\u7a0b\u5ea6\u548c\u5f71\u54cd\u529b\u3002<\/p>\n\n\n\n

        \n
      • ape R\u5305\u4ecb\u7ecd<\/em><\/strong><\/em><\/strong><\/em><\/strong><\/em><\/strong><\/li>\n<\/ul>\n\n\n\n

        APE\uff08Analysis of Phylogenetics and Evolution\uff09\u662f\u4e00\u4e2a\u7528\u4e8e\u5206\u5b50\u8fdb\u5316\u548c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u514d\u8d39R\u8f6f\u4ef6\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u591a\u79cd\u7528\u4e8e\u5904\u7406\u548c\u5206\u6790\u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u51fd\u6570\u548c\u65b9\u6cd5\uff0c\u6db5\u76d6\u4e86\u4ece\u8ba1\u7b97\u8fdb\u5316\u8ddd\u79bb\u3001\u91cd\u5efa\u57fa\u56e0\u6811\u5230\u6bd4\u8f83\u6570\u636e\u5206\u6790\u3001\u8fdb\u5316\u901f\u7387\u4f30\u8ba1\u7b49\u591a\u4e2a\u65b9\u9762\u3002<\/p>\n\n\n\n

          \n
        • \u6838\u5fc3\u529f\u80fd\u53ca\u7279\u70b9\uff1a<\/em><\/strong><\/em><\/strong><\/em><\/strong><\/em><\/strong><\/li>\n\n\n\n
        • \u5f3a\u5927\u7684\u6570\u636e\u5904\u7406\u80fd\u529b\uff1aAPE\u80fd\u591f\u8bfb\u53d6\u548c\u5199\u5165\u591a\u79cd\u6570\u636e\u683c\u5f0f\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\uff0c\u5e76\u652f\u6301\u591a\u79cd\u7c7b\u578b\u7684\u8fdb\u5316\u5206\u6790\u3002<\/li>\n\n\n\n
        • \u4e30\u5bcc\u7684\u7edf\u8ba1\u65b9\u6cd5\uff1aAPE\u63d0\u4f9b\u4e86\u591a\u79cd\u7528\u4e8e\u6bd4\u8f83\u548c\u7fa4\u4f53\u9057\u4f20\u5206\u6790\u7684\u9ad8\u7ea7\u7edf\u8ba1\u65b9\u6cd5\uff0c\u5982\u8ddd\u79bb\u77e9\u9635\u8ba1\u7b97\u3001\u7956\u5148\u72b6\u6001\u91cd\u5efa\u7b49\u3002<\/li>\n\n\n\n
        • \u6613\u4e8e\u6269\u5c55\uff1aAPE\u57fa\u4e8eR\u8bed\u8a00\u7684\u5f00\u6e90\u6846\u67b6\uff0c\u7528\u6237\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u8981\u7f16\u5199\u989d\u5916\u7684\u51fd\u6570\u548c\u811a\u672c\u6765\u6269\u5c55\u5176\u529f\u80fd\u3002<\/li>\n<\/ul>\n\n\n\n

          l ape R\u5305\u4f5c\u4e3a\u5206\u5b50\u8fdb\u5316\u548c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u9886\u57df\u7684\u91cd\u8981\u5de5\u5177\uff0c\u5728\u79d1\u7814\u754c\u6709\u7740\u5e7f\u6cdb\u7684\u5e94\u7528\u548c\u6df1\u8fdc\u7684\u5f71\u54cd\u3002\u5b83\u4e3a\u6211\u4eec\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5f3a\u5927\u800c\u7075\u6d3b\u7684\u5e73\u53f0\u6765\u63a2\u7d22\u751f\u7269\u4e4b\u95f4\u7684\u8fdb\u5316\u5173\u7cfb\u3002<\/p>\n\n\n\n

          \u4e8c\u3001 <\/strong>\u4ee3\u7801\u5b9e\u64cd<\/strong><\/strong><\/h3>\n\n\n\n

          \u5c0f\u679c\u5c06\u5e26\u5c0f\u4f19\u4f34\u4eec\u8fdb\u884c\u4ee3\u7801\u5b9e\u6218\uff1a\u7ed8\u5236\u4f60\u7684\u8fdb\u5316\u6811\uff0c\u53ea\u9700\u51e0\u884c\u4ee3\u7801\uff0c\u4f60\u5c31\u80fd\u8f7b\u677e\u8bfb\u53d6\u6570\u636e\u3001\u6784\u5efa\u5e76\u53ef\u89c6\u5316\u4f60\u7684\u8fdb\u5316\u6811\u3002ggtree\u4e0eape\u5305\u7684\u7ed3\u5408\uff0c\u5c06\u4f1a\u8ba9\u8fd9\u4e00\u8fc7\u7a0b\u53d8\u5f97\u8f7b\u677e\u6109\u5feb~\u672c\u6b21\u4ecb\u7ecd\u7684R\u5305\u64cd\u4f5c\u4f1a\u5360\u7528\u5185\u5b58\u8f83\u5927\uff0c\u5c0f\u679c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u5c0f\u4f19\u4f34\u4eec\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\u6027\u4ef7\u6bd4\u5c45\u9ad8\u7684\u670d\u52a1\u5668\uff01<\/strong><\/p>\n\n\n\n

            \n
          • \u5b89\u88c5\u548c\u52a0\u8f7d\u6240\u9700\u7684\u5305\uff1a<\/strong>\u9996\u5148\u68c0\u67e5ggtree\u548cape\u5305\u662f\u5426\u5df2\u5b89\u88c5\uff0c\u5982\u679c\u672a\u5b89\u88c5\u5219\u8fdb\u884c\u5b89\u88c5\uff0c\u5e76\u52a0\u8f7d\u8fd9\u4e24\u4e2a\u5305\u4ee5\u4fbf\u4f7f\u7528<\/strong><\/li>\n<\/ul>\n\n\n\n

            if (!requireNamespace(“ggtree”, quietly = TRUE)) {<\/p>\n\n\n\n

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

            }<\/p>\n\n\n\n

            library(ggtree)<\/p>\n\n\n\n

            if (!requireNamespace(“ape”, quietly = TRUE)) {<\/p>\n\n\n\n

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

            }<\/p>\n\n\n\n

            library(ape)<\/p>\n\n\n\n

              \n
            • \u6811<\/strong>\u6587\u4ef6\u7684\u8bfb\u5165<\/strong><\/li>\n<\/ul>\n\n\n\n

              setwd(“”D:\/A)<\/p>\n\n\n\n

              tree1 <- read.tree(“D:\/A\/tree1.nwk”)<\/p>\n\n\n\n

              tree2 <- read.tree(“D:\/A\/tree2.nwk”)<\/p>\n\n\n\n

              tree3 <- read.tree(“D:\/A\/tree3.nwk”)<\/p>\n\n\n\n

              \"\"<\/figure>\n\n\n\n
                \n
              • \u6811\u7684\u53ef\u89c6\u5316\uff1a<\/strong>\u4f7f\u7528ggtree\u51fd\u6570\u7ed3\u5408geom_tiplab\u548cgeom_nodepoint\u51fd\u6570\u6765\u7ed8\u5236\u6811\uff0c\u5e76\u4e3a\u53f6\u8282\u70b9\u6807\u7b7e\u548c\u8282\u70b9\u70b9\u8bbe\u7f6e\u989c\u8272\u548c\u5927\u5c0f\u3002\u4e3a\u6bcf\u68f5\u6811\u8bbe\u7f6e\u4e0d\u540c\u7684\u4e3b\u9898\u548c\u6807\u9898\u3002<\/strong><\/li>\n<\/ul>\n\n\n\n

                p1 <- ggtree(tree1) +<\/p>\n\n\n\n

                  geom_tiplab(aes(color = “orange”), size = 3) +<\/p>\n\n\n\n

                  geom_nodepoint(color = “skyblue”, size = 3) +<\/p>\n\n\n\n

                  theme_tree2() +<\/p>\n\n\n\n

                  ggtitle(“Phylogenetic Tree1 with Branch Lengths”)<\/p>\n\n\n\n

                print(p1)<\/p>\n\n\n\n

                \"\"<\/figure>\n\n\n\n

                \u7ed8\u5236\u7684\u8fdb\u5316\u6811\u901a\u8fc7\u4e00\u7cfb\u5217\u8282\u70b9\u5c55\u793a\u4e86t1~t20\u4e4b\u95f4\u7684\u8fdb\u5316\u5173\u7cfb\u3002\u6bcf\u4e2a\u8282\u70b9\u4ee3\u8868\u4e00\u4e2a\u5206\u7c7b\u5355\u5143\uff0c\u8868\u793a\u4e0d\u540c\u79cd\u7684\u7269\u79cd\u3002\u8282\u70b9\u901a\u8fc7\u989c\u8272\u7f16\u7801\u8fdb\u884c\u533a\u5206\uff0c\u4ee3\u8868\u4e0d\u540c\u7684\u8fdb\u5316\u652f\u6216\u7fa4\u4f53\u3002\u5c0f\u679c\u5229\u7528\u989c\u8272\u7f16\u7801\uff0c\u6709\u52a9\u4e8e\u8bc6\u522b\u4e0d\u540c\u7684\u8fdb\u5316\u7fa4\u4f53\u3002<\/p>\n\n\n\n

                p2 <- ggtree(tree2) +<\/p>\n\n\n\n

                  geom_tiplab(aes(color = “yellow”), size = 5) +<\/p>\n\n\n\n

                  geom_nodepoint(color = “green”, size = 3) +<\/p>\n\n\n\n

                  theme_tree2() +<\/p>\n\n\n\n

                  ggtitle(“Phylogenetic Tree2 with Branch Lengths”)<\/p>\n\n\n\n

                print(p2)<\/p>\n\n\n\n

                \"\"<\/figure>\n\n\n\n

                \u7ed8\u5236\u7684\u8fdb\u5316\u6811\u901a\u8fc7\u4e00\u7cfb\u5217\u6709\u5e8f\u7684\u8282\u70b9\uff0c\u5982t2\u81f3t30\uff0c\u63cf\u7ed8\u4e86\u4ece\u5171\u540c\u7956\u5148\u5206\u5316\u51fa\u7684\u7269\u79cd\u95f4\u7684\u8fdb\u5316\u8def\u5f84\u3002\u6bcf\u4e2a\u8282\u70b9\u4ee3\u8868\u4e00\u4e2a\u7279\u5b9a\u7684\u5206\u7c7b\u5355\u5143\uff0c\u5bf9\u5e94\u4e00\u4e2a\u7269\u79cd\u6216\u7269\u79cd\u7fa4\u3002\u989c\u8272\u7f16\u7801\uff0c\u4e3a\u6211\u4eec\u8bc6\u522b\u4e0d\u540c\u7684\u8fdb\u5316\u652f\u63d0\u4f9b\u4e86\u76f4\u89c2\u7684\u89c6\u89c9\u533a\u5206\u7406\u89e3\u7269\u79cd\u95f4\u7684\u4eb2\u7f18\u5173\u7cfb\u3002\u901a\u8fc7\u8fd9\u4e9b\u989c\u8272\uff0c\u6211\u4eec\u53ef\u8ffd\u8e2a\u7279\u5b9a\u7279\u5f81\u6216\u9002\u5e94\u6027\u5728\u8fdb\u5316\u8fc7\u7a0b\u4e2d\u7684\u5206\u5e03\u3002<\/p>\n\n\n\n

                p3 <- ggtree(tree3) +<\/p>\n\n\n\n

                  geom_tiplab(aes(color = “red”), size = 4) +<\/p>\n\n\n\n

                  geom_nodepoint(color = “blue”, size = 3) +<\/p>\n\n\n\n

                  theme_tree2() +<\/p>\n\n\n\n

                  ggtitle(“Phylogenetic Tree3 with Branch Lengths”)<\/p>\n\n\n\n

                print(p3)<\/p>\n\n\n\n

                \"\"<\/figure>\n\n\n\n

                \u7ed8\u5236\u51fa\u7684\u8fdb\u5316\u6811\u901a\u8fc7\u4e00\u7cfb\u5217\u8282\u70b9\uff08\u6807\u8bc6\u4e3at10\u81f3t25\u4ee5\u53ca\u7279\u5f02\u7684t2\u548ct1\uff09\u7cbe\u7ec6\u523b\u753b\u4e86\u751f\u7269\u5206\u7c7b\u5355\u5143\u7684\u7cfb\u7edf\u53d1\u80b2\u67b6\u6784\u3002\u6bcf\u4e2a\u8282\u70b9\u8c61\u5f81\u7740\u4e00\u4e2a\u72ec\u7279\u7684\u751f\u7269\u5206\u7c7b\u5b9e\u4f53\uff0c\u53ef\u80fd\u4ee3\u8868\u5355\u4e00\u7269\u79cd\u6216\u5176\u4e9a\u79cd\u7fa4\u3002\u5c0f\u679c\u5e94\u7528\u989c\u8272\u7f16\u7801\uff0c\u8fd9\u6837\u53ef\u4ee5\u4e3a\u89c6\u89c9\u8fa8\u8bc6\u63d0\u4f9b\u8f85\u52a9\uff0c\u79d1\u5b66\u5212\u5206\u4e0d\u540c\u7684\u7cfb\u7edf\u53d1\u80b2\u652f\u7cfb\u3002\u8fd9\u79cd\u7f16\u7801\u7b56\u7565\u53ef\u4ee5\u63ed\u793a\u51fa\u7269\u79cd\u95f4\u7684\u4eb2\u7f18\u5173\u7cfb\u548c\u6f5c\u5728\u7684\u8fdb\u5316\u8def\u5f84\u3002<\/p>\n\n\n\n

                  \n
                • \u6dfb\u52a0\u5206\u652f\u957f\u5ea6\u6807\u7b7e\uff1a<\/strong>\u4f7f\u7528geom_text\u51fd\u6570\u5728p1\u5bf9\u8c61\u4e0a\u6dfb\u52a0\u5206\u652f\u957f\u5ea6\u6807\u7b7e\u3002\uff0c\u56e0\u4e3abranch.length\u76f4\u63a5\u5728aes()\u51fd\u6570\u4e2d\u521b\u5efa\u3002<\/strong><\/li>\n<\/ul>\n\n\n\n

                  P1 <- p1 + geom_text(aes(label = branch.length), vjust = -1)<\/p>\n\n\n\n

                  print(P1)<\/p>\n\n\n\n

                  \u548c\u5c0f\u679c\u4e00\u8d77\u770b\u770b\u7ed3\u679c\u5427\uff01<\/em><\/strong><\/em><\/strong><\/em><\/strong><\/em><\/strong><\/p>\n\n\n\n

                  \"\"<\/figure>\n\n\n\n

                  \u8fd9\u68f5\u7cfb\u7edf\u53d1\u80b2\u6811\u4ee5\u7cbe\u786e\u7684\u5206\u652f\u957f\u5ea6\u4e3a\u7279\u5f81\uff0c\u5c55\u793a\u4e86\u4ece\u5171\u540c\u7956\u5148\u6f14\u5316\u800c\u6765\u7684\u751f\u7269\u5206\u7c7b\u5355\u5143\u95f4\u7684\u76f8\u5e94\u7684\u590d\u6742\u5173\u7cfb\u3002\u5206\u652f\u957f\u5ea6\uff08\u59820.439831687603146\u81f30.810064353048801\uff09\u91cf\u5316\u4e86\u7269\u79cd\u95f4\u9057\u4f20\u5dee\u5f02\u7684\u7a0b\u5ea6\uff0c\u53cd\u6620\u4e86\u5b83\u4eec\u5728\u8fdb\u5316\u5386\u7a0b\u4e2d\u7684\u76f8\u5bf9\u65f6\u95f4\u8ddd\u79bb\u3002\u8282\u70b9t17\u548ct18\u6807\u8bc6\u4e86\u7279\u5b9a\u7684\u8fdb\u5316\u5206\u652f\uff0c\u8fd9\u91cc\u5c0f\u679c\u4f9d\u65e7\u4f7f\u7528\u4e86\u989c\u8272\u7f16\u7801\u4e3a\u533a\u5206\u4e0d\u540c\u7684\u8fdb\u5316\u652f\u6216\u751f\u6001\u4f4d\u63d0\u4f9b\u4e86\u76f4\u89c2\u7684\u5206\u7c7b\u5de5\u5177\u3002<\/p>\n\n\n\n

                    \n
                  • \u8282\u70b9\u5927\u5c0f\u6839\u636e\u652f\u6301\u5ea6\u8c03\u6574\uff1a<\/strong>\u5c0f\u679c\u5728\u4ee3\u7801\u4e2d\u521b\u5efa\u4e86\u4e00\u4e2a\u540d\u4e3anode_sizes\u7684\u5411\u91cf\uff0c\u6839\u636e\u652f\u6301\u5ea6\u8c03\u6574\u8282\u70b9\u5927\u5c0f\uff0c\u6dfb\u52a0\u8282\u70b9\u5927\u5c0f\u6839\u636e\u652f\u6301\u5ea6<\/li>\n<\/ul>\n\n\n\n

                    node_sizes <- 2 + (node_labels$support \/ max(node_labels$support)) * 10<\/p>\n\n\n\n

                    p1 <- p1 + geom_nodepoint(aes(size = support), color = “black”, size = 3)<\/p>\n\n\n\n

                      \n
                    • \u56fe\u4f8b\u6dfb\u52a0\uff1a<\/strong>\u6dfb\u52a0\u4e00\u4e2a\u56fe\u4f8b\uff0c\u4f7f\u7528\u662fgeom_text\u3002<\/strong><\/li>\n<\/ul>\n\n\n\n

                      legend_title <- “Branch Length Legend”<\/p>\n\n\n\n

                      p1 <- p1 + geom_text(aes(label = legend_title), x = 0.8, y = 0.7, size = 12)<\/p>\n\n\n\n

                        \n
                      • \u8c03\u6574\u5e03\u5c40\u4e3a\u5706\u5f62\uff1a<\/strong> \u8c03\u6574\u5e03\u5c40\u4e3a\u5706\u5f62<\/li>\n<\/ul>\n\n\n\n

                        p1 <- ggtree(tree1, layout = “circular”)<\/p>\n\n\n\n

                        print(p1)<\/p>\n\n\n\n

                        \"\"<\/figure>\n\n\n\n
                          \n
                        • \u8ba1\u7b97\u8282\u70b9\u6df1\u5ea6\u548c\u751f\u6210\u8282\u70b9\u6807\u7b7e\uff1a<\/strong>\u8ba1\u7b97\u4e86tree2\u7684\u8282\u70b9\u6df1\u5ea6\uff0c\u5e76\u751f\u6210\u4e86\u4e00\u4e2a\u5305\u542b\u6807\u7b7e\u548c\u968f\u673a\u652f\u6301\u5ea6\u7684\u6570\u636e\u6846node_labels\u3002<\/li>\n<\/ul>\n\n\n\n

                          node_depths <- node.depth(tree2)<\/p>\n\n\n\n

                          node_labels <- data.frame(<\/p>\n\n\n\n

                            label = paste(“Node”, 1:length(node_depths), sep = ” “),<\/p>\n\n\n\n

                            support = runif(length(node_depths)) * 100 )<\/p>\n\n\n\n

                          \"\"<\/figure>\n\n\n\n
                            \n
                          • \u5206\u652f\u957f\u5ea6\u6807\u7b7e\u6dfb\u52a0\u5230\u7b2c\u4e00\u4e2a\u6811\uff1a<\/strong>\u8fd9\u90e8\u5206\u4ee3\u7801\u4e3atree2\u6dfb\u52a0\u5206\u652f\u957f\u5ea6\u6807\u7b7e\uff0cbranch_length\u5728aes()\u4e2d\u5b9a\u4e49\u3002<\/li>\n<\/ul>\n\n\n\n

                            branch_lengths <- tree2$edge.length<\/p>\n\n\n\n

                            P1 <- ggtree(tree2, aes(branch.length = branch_lengths)) +<\/p>\n\n\n\n

                              geom_text(aes(label = branch_length), vjust = -1) +<\/p>\n\n\n\n

                              theme_minimal()<\/p>\n\n\n\n

                            \"\"<\/figure>\n\n\n\n
                              \n
                            • \u67e5\u627e\u652f\u6301\u5ea6\u5927\u4e8e50\u7684\u8282\u70b9\u5e76\u6253\u5370\u6807\u7b7e\uff1a<\/strong>\u627e\u51fanode_labels\u4e2d\u652f\u6301\u5ea6\u5927\u4e8e50\u7684\u8282\u70b9\uff0c\u5e76\u6253\u5370\u8fd9\u4e9b\u8282\u70b9\u7684\u6807\u7b7e\u3002<\/li>\n<\/ul>\n\n\n\n

                              high_support_nodes <- which(node_labels$support > 50)<\/p>\n\n\n\n

                              high_support_labels <- node_labels$label[high_support_nodes]<\/p>\n\n\n\n

                                \n
                              • \u7a81\u51fa\u663e\u793a\u652f\u6301\u5ea6\u5927\u4e8e50\u7684\u8282\u70b9\uff1a<\/strong>\u5f15\u7528node_labels\u4e2d\u7684\u6570\u636e\u521b\u5efa\u4e00\u4e2a\u65b0\u7684\u6811\u5bf9\u8c61P4\u6765\u7a81\u51fa\u663e\u793a\u652f\u6301\u5ea6\u5927\u4e8e50\u7684\u8282\u70b9\u3002<\/strong><\/li>\n<\/ul>\n\n\n\n

                                print(high_support_labels)<\/p>\n\n\n\n

                                \"\"<\/figure>\n\n\n\n

                                P4 <- p1 + geom_nodepoint(aes(size = support), color = “red”, size = 3)<\/p>\n\n\n\n

                                print(P4)<\/p>\n\n\n\n

                                \"\"<\/figure>\n\n\n\n
                                  \n
                                • \u4fdd\u5b58\u56fe\u50cf<\/strong><\/strong><\/li>\n<\/ul>\n\n\n\n

                                  ggsave(“Phylogenetic_Tree2_with_Node_Labels_and_Support.png”, p2, width = 10, height = 8, dpi = 300)<\/p>\n\n\n\n

                                  ggssave(“Phylogenetic_Tree1.png”, p1, width = 10, height = 8)<\/p>\n\n\n\n

                                  ggsave(“Phylogenetic_Tree2.png”, p2, width = 10, height = 8)<\/p>\n\n\n\n

                                  ggsave(“Phylogenetic_Tree3.png”, p3, width = 10, height = 8)<\/p>\n\n\n\n

                                  \u4e09\u3001 <\/strong>\u6587\u7ae0\u5c0f\u7ed3<\/strong><\/strong><\/h3>\n\n\n\n

                                  \u672c\u671f\u5c0f\u679c\u548c\u5c0f\u4f19\u4f34\u4eec\u4e00\u8d77\u5229\u7528ggtree\u548cape\u5305\uff0c\u7cbe\u5fc3\u6253\u9020\u4e86\u51e0\u68f5\u7cfb\u7edf\u53d1\u80b2\u6811\u3002\u6574\u4f53\u800c\u8a00\uff0c\u8fd9\u51e0\u68f5\u6811\u63d0\u4f9b\u4e00\u4e2a\u5173\u4e8e\u7269\u79cd\u591a\u6837\u6027\u548c\u8fdb\u5316\u5386\u53f2\u7684\u5b8f\u89c2\u89c6\u89d2\u3002\u672c\u671f\u5229\u7528ggtree\u5305\uff0c\u6211\u4eec\u4e3a\u6bcf\u68f5\u6811\u6dfb\u52a0\u4e86\u8272\u5f69\u548c\u7ec6\u8282\uff0c\u901a\u8fc7geom_tiplab\u548cgeom_nodepoint\u51fd\u6570\u4e3a\u53f6\u6807\u7b7e\u548c\u8282\u70b9\u70b9\u8d4b\u4e88\u4e86\u751f\u52a8\u7684\u89c6\u89c9\u8868\u73b0\u3002\u6211\u4eec\u8fd8\u4e3a\u5206\u652f\u957f\u5ea6\u6807\u6ce8\u4e86\u6807\u7b7e\uff0c\u5e76\u5b9a\u5236\u4e86\u56fe\u4f8b\uff0c\u4f7f\u4fe1\u606f\u4f20\u8fbe\u66f4\u4e3a\u6e05\u6670\u3002\u4e3a\u4e86\u63d0\u5347\u8282\u70b9\u7684\u53ef\u89c6\u5316\u6548\u679c\uff0c\u6211\u4eec\u521b\u5efa\u4e86\u4e00\u4e2a\u5305\u542b\u652f\u6301\u5ea6\u4fe1\u606f\u7684\u6570\u636e\u6846node_labels\uff0c\u5e76\u6839\u636e\u652f\u6301\u5ea6\u52a8\u6001\u8c03\u6574\u4e86\u8282\u70b9\u5927\u5c0f\uff0c\u8ba9\u6811\u7684\u7ed3\u6784\u66f4\u52a0\u76f4\u89c2\u3002\u6700\u540e\uff0c\u6211\u4eec\u4fdd\u5b58\u4e86\u8fd9\u4e9b\u7cbe\u5fc3\u5236\u4f5c\u7684\u56fe\u50cf\uff0c\u8bb0\u5f55\u4e0b\u8fd9\u6b21\u63a2\u7d22\u7684\u6210\u679c\u3002ggtree\u4e0eape\u5305\u662f\u63a2\u7d22\u751f\u7269\u8fdb\u5316\u7684\u5f97\u529b\u52a9\u624b\uff0c\u8fd9\u4e24\u4e2aR\u5305\u8ba9\u6211\u4eec\u80fd\u591f\u4ece\u5fae\u89c2\u5230\u5b8f\u89c2\uff0c\u6df1\u5165\u89e3\u6790\u751f\u547d\u7684\u5965\u79d8\u3002\u5982\u679c\u4f60\u5bf9\u751f\u7269\u4fe1\u606f\u5b66\u5145\u6ee1\u5174\u8da3\uff0c\u6216\u6e34\u671b\u66f4\u6df1\u523b\u5730\u7406\u89e3\u751f\u547d\u6f14\u53d8\uff0c\u4e0d\u59a8\u4eb2\u81ea\u5c1d\u8bd5\u8fd9\u4e9b\u5de5\u5177\uff0c\u5f00\u542f\u4f60\u7684\u53d1\u73b0\u4e4b\u65c5\uff01\u6700\u540e\u5982\u679c\u5404\u4f4d\u5c0f\u4f19\u4f34\u4eec\u89c9\u5f97\u81ea\u5df1\u8fd0\u884c\u4ee3\u7801\u592a\u9ebb\u70e6\uff0c\u6b22\u8fce\u7528\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u51fa\u60f3\u8981\u7684\u56fe\u54e6\uff0c\u9644\u4e91\u751f\u4fe1\u94fe\u63a5\uff08http:\/\/www.biocloudservice.com\/home.html\uff09\u3002<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

                                  \u5927\u5bb6\u597d~\u6211\u662f\u5c0f\u679c!\u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u662f\u5426\u548c\u5c0f\u679c\u4e00\u6837\u5bf9\u751f\u7269\u7684\u8d77\u6e90\u548c\u53d1\u5c55\u597d\u5947\u5462\uff1f\u5b83\u4eec\u662f\u5982\u4f55\u4ece\u8fdc\u53e4\u65f6\u671f\u6f14\u5316\u81f3\u4eca\uff0c\u5f62\u6210\u4e86\u4eca […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/61531"}],"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=61531"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61531\/revisions"}],"predecessor-version":[{"id":61542,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61531\/revisions\/61542"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61531"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61531"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61531"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}