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data-username=\"v2_060000231003b20faec8c7e38019c0d4cc02ec33b077ef3bc1e59b4a7f53fd21ec5cd455628a@finder\" data-nickname=\"\u4e91\u751f\u4fe1\u5b66\u751f\u7269\u4fe1\u606f\u5b66\" data-desc=\"\u5c06\u572807\u670824\u65e5 15:00 \u76f4\u64ad\" data-livewording=\"\u9884\u7ea6\" data-intro=\"\u57fa\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5bf9\u4e8e\u7269\u79cdLncRNA\u7684\u9274\u5b9a\" data-type=\"live\" data-status=\"0\" data-noticeid=\"finderlivenotice-v2_060000231003b20faec8c7e38019c0d4cc02ec33b077ef3bc1e59b4a7f53fd21ec5cd455628a@finder-1689834339958814-1998268070\"><\/mp-common-videosnap><\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e3b\u8981\u64cd\u4f5c\u5185\u5bb9<\/span><\/em><\/strong><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">1\u3001R\u73af\u5883\u7684\u914d\u7f6e\u4ee5\u53caR\u5305\u7684\u4e0b\u8f7d<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">R\u8bed\u8a00\u4e0b\u8f7d\u5730\u5740\uff1a<\/span><\/strong><span style=\"font-size: 14px;\">https:\/\/www.r-project.org\/<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">Rstudio<\/span><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">\u4e0b\u8f7d\u5730\u5740\uff1a<\/span><\/strong><span style=\"font-size: 14px;\">https:\/\/www.rstudio.com\/products\/rstudio\/download\/#download<\/span><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">R\u5305\u7684\u5b89\u88c5\uff1a<\/span><\/strong><span style=\"font-size: 14px;letter-spacing: 0.034em;\">ggClusterNet\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u9700\u8981\u5f88\u591a\u4f9d\u8d56\u7684\u5b89\u88c5\u5305\uff0c\u8017\u65f6\u4f1a\u4e45\u4e00\u4e9b\uff0c\u5e0c\u671b\u4f60\u8010\u5fc3\u7b49\u5f85\uff08\u5b89\u88c5\u901f\u5ea6\u53d6\u51b3\u4f60\u7684R\u73af\u5883\u4e2d\u4f9d\u8d56\u5305\u6709\u591a\u5c11\u4e2a\u4ee5\u524d\u6ca1\u6709\u4e0b\u8f7d\u8fc7\u54e6\uff5e\uff09<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5b89\u88c5<span class=\"code-snippet__function\">ggClusterNet<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__title\">devtools::install_github<\/span><span class=\"code-snippet__params\">(<span class=\"code-snippet__string\">\"taowenmicro\/ggClusterNet\"<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">2\u3001\u6784\u5efa\u6570\u636e\u683c\u5f0f<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u52a0\u8f7d\u6240\u7528\u7684\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggClusterNet)<\/span><\/code><code><span class=\"code-snippet_outer\">library(phyloseq)<\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(igraph)<\/span><\/code><code><span class=\"code-snippet_outer\">library(sna)<\/span><\/code><code><span class=\"code-snippet_outer\">library(network)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6839\u636e\u81ea\u5df1\u7684\u6570\u636e\u683c\u5f0f\u5206\u522b\u5bfc\u5165otuable\u3001taxnomoy\u548cmetadata\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">otutable <- read.table(<span class=\"code-snippet__string\">\"table.xls\"<\/span>, header = T, sep = <span class=\"code-snippet__string\">\"t\"<\/span>,row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">taxnomoy <- read.table(<span class=\"code-snippet__string\">\"tax.txt\"<\/span>, header = T,sep = <span class=\"code-snippet__string\">\"t\"<\/span>, fill=TRUE, na.strings = <span class=\"code-snippet__string\">\"NA\"<\/span>, row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- read.table(<span class=\"code-snippet__string\">\"metadata.tsv\"<\/span>, header = T,sep = <span class=\"code-snippet__string\">\"t\"<\/span>, row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6700\u540e\u5f97\u5230ps\u7684\u6570\u636e\u683c\u5f0f<\/span><\/code><code><span class=\"code-snippet_outer\">ps <- phyloseq(sample_data(metadata),otu_table(as.matrix(otutable),taxa_are_rows = T),tax_table(as.matrix(taxnomoy)))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6784\u5efa\u597d\u540e\u53ef\u4ee5ps\u4e00\u4e0b\u770b\u4e00\u4e0b\u8fd9\u4e2a\u6570\u636e\u96c6(\u4e3b\u8981\u5305\u62ecotu_table()\u3001sample_table()\u3001tax_table()\u3001phy_table()\u56db\u4e2a\u90e8\u5206\uff09<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6570\u636e\u96c6\u7684\u6784\u5efa\u662f\u6700\u9ebb\u70e6\u7684\u5730\u65b9\u4f46\u662f\u4e00\u65e6\u6784\u5efa\u597d\uff0c\u64cd\u4f5c\u8d77\u6765\u5c31\u5f88\u65b9\u4fbf\uff0c\u5e0c\u671b\u4f60\u8010\u5fc3\u505a\u597d\u8fd9\u4e00\u6b65\uff5e<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u6784\u5efa\u597d\u6570\u636e\u683c\u5f0f\u540e\uff0c\u505a\u5171\u73b0\u7f51\u7edc\u5206\u6790\u53ea\u9700\u4e00\u884c\u4ee3\u7801\u5c31\u53ef\u4ee5\u641e\u5b9a\uff0c\u5feb\u6765\u8bd5\u4e00\u4e0b\uff5e<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">3\u3001\u4e00\u952e\u5206\u6790<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5148\u521b\u5efa\u4e00\u4e2a\u5b58\u50a8\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">path1 = <span class=\"code-snippet__string\">\".\/result_net\/\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dir.create(path1)<\/span><\/code><code><span class=\"code-snippet_outer\">result1 = network<span class=\"code-snippet__number\">.2<\/span>(ps = ps,#\u6784\u5efa\u7684\u6570\u636e\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\"> N = <span class=\"code-snippet__number\">100<\/span>, #\u53d6\u524d\u4e30\u5ea6\u6700\u9ad8\u7684\u524d<span class=\"code-snippet__number\">100<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> layout_net = <span class=\"code-snippet__string\">\"model_Gephi.2\"<\/span>, #\u5e03\u5c40\u683c\u5f0fmodel_Gephi<span class=\"code-snippet__number\">.2<\/span>\u8fd9\u91cc\u6211\u7528\u7684Gephi\u7684<\/span><\/code><code><span class=\"code-snippet_outer\"> r.threshold=<span class=\"code-snippet__number\">0.6<\/span>, #\u76f8\u5173\u6027\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"> p.threshold=<span class=\"code-snippet__number\">0.01<\/span>, #\u663e\u8457\u6027\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"> label = TRUE, #\u662f\u5426\u5728\u8282\u70b9\u4e0a\u6807\u8bb0\u6807\u7b7e<\/span><\/code><code><span class=\"code-snippet_outer\"> path = path1, #\u5b58\u653e\u7684\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"> lab = <span class=\"code-snippet__string\">\"Genus\"<\/span>, #\u6807\u7b7e\u7528Genus \u8fd9\u91cc\u4e00\u5b9a\u8981\u4e0etaxnomoy\u4e2d\u5217\u540d\u4e00\u81f4<\/span><\/code><code><span class=\"code-snippet_outer\"> zipi = TRUE #\u662f\u5426\u7ed8\u5236zipi\u56fe)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">4\u3001\u8f93\u51fa\u6587\u4ef6\u89e3\u8bfb<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">1\u3001\u6709\u4e24\u5f20pdf\u7684\u5173\u8054\u7f51\u7edc\u56fe<span style=\"font-size: 14px;color: rgb(61, 170, 214);\">(networkXX.pdf)<\/span>\uff0c\u662f\u6839\u636e\u5305\u4e2d\u9ed8\u8ba4\u7684\u53c2\u6570\u7ed8\u5236\u7684\uff0c\u4f46\u662f\u4e00\u822c\u56fe\u5f62\u8fbe\u4e0d\u5230\u60f3\u8981\u7684\u7406\u60f3\u6548\u679c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">2\u3001\u4f1a\u8f93\u51fa\u53ef\u4ee5\u5bfc\u5165\u5230Gephi\u4e2d\u7684\u8fb9\u6587\u4ef6\u548c\u70b9\u6587\u4ef6<span style=\"font-size: 14px;color: rgb(61, 170, 214);\">\uff08XX_Gephi_edge.csv\u3001XX_Gephi_node.csv\uff09<\/span>,\u53ef\u4ee5\u5bfc\u5165\u5230Gephi\u8fdb\u884c\u8c03\u8282\u56fe\u7684\u5e03\u5c40\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">5\u3001\u51fa\u7248\u7ea7\u56fe\u5f62\u89e3\u8bfb<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5982\u4e0b\u56fe\u5373\u4e3a\u6700\u540eGephi\u505a\u51fa\u7684\u56fe\uff1a\u6bcf\u4e2a\u8282\u70b9\u4ee3\u8868\u4e00\u4e2a\u5fae\u751f\u7269\u7684\u5c5e\u6c34\u5e73\uff0c\u989c\u8272\u4ee3\u8868\u5c5e\u6240\u5728\u7684\u95e8\u7c7b\uff0c\u5927\u5c0f\u4ee3\u8868\u5c5e\u7684\u76f8\u5bf9\u4e30\u5ea6\uff0c\u4e24\u4e2a\u5c5e\u6c34\u5e73\u4e4b\u95f4\u6b63\u76f8\u5173\u7528\u7ea2\u8272\u8fde\u63a5\uff0c\u8d1f\u76f8\u5173\u7528\u84dd\u8272\u8fde\u63a5\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_eAsqO1krcxHaDOXEV0SMgVVYBD4h0Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyL6u7wJswOp8vtpzGp6vYnKf4rIYDhaib4HWqRWFt60sKD8eAsqO1krcxHaDOXEV0SMgVVYBD4h0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">ggClusterNet\u7684\u5305\u5bf9\u5173\u8054\u7f51\u7edc\u7684\u5e03\u5c40\u4ee5\u53ca\u4e00\u4e9b\u62d3\u6251\u5b66\u6307\u6570\u7684\u8ba1\u7b97\u90fd\u5177\u6709\u76f8\u5e94\u7684\u529f\u80fd\uff0c\u5982\u679c\u60f3\u7ed8\u5236\u51fa\u6ee1\u610f\u7684\u5173\u8054\u7f51\u7edc\u56fe\uff0c\u5c31\u7528\u591a\u591a\u63a2\u7d22\uff0c\u8fd9\u91cc\u53ea\u662f\u7b80\u5355\u7684\u7ed8\u5236\u51fa\u7f51\u7edc\u56fe\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u597d\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5173\u8054\u7f51\u7edc\u56fe\u5c31\u5b8c\u6210\u4e86\u3002\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u5c31\u548c\u5c0f\u679c\u8ba8\u8bba\u5427\uff5e<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"578\" data-cropsely1=\"0\" data-cropsely2=\"322\" data-galleryid=\"\" data-ratio=\"0.7193195625759417\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_oRxs73HBHUoxCtAqBPQnq1AXricRvg-8.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxenwVZiaibuOTpj6MMDUj2LoPdS6tic40bbGQV7QyM6QOQY8EFoRxs73HBHUoxCtAqBPQnq1AXricRvg\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"823\" style=\"width: 578px;height: 416px;\" data-recalc-dims=\"1\"><\/p>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e00\u952e\u7ed8\u5236\u5fae\u751f\u7269\u5173\u8054\u7f51\u5171\u73b0\u56fe \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c &nbs […]<\/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\/59083"}],"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=59083"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59083\/revisions"}],"predecessor-version":[{"id":59087,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59083\/revisions\/59087"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59083"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59083"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59083"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

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data-username=\"v2_060000231003b20faec8c7e38019c0d4cc02ec33b077ef3bc1e59b4a7f53fd21ec5cd455628a@finder\" data-nickname=\"\u4e91\u751f\u4fe1\u5b66\u751f\u7269\u4fe1\u606f\u5b66\" data-desc=\"\u5c06\u572807\u670824\u65e5 15:00 \u76f4\u64ad\" data-livewording=\"\u9884\u7ea6\" data-intro=\"\u57fa\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5bf9\u4e8e\u7269\u79cdLncRNA\u7684\u9274\u5b9a\" data-type=\"live\" data-status=\"0\" data-noticeid=\"finderlivenotice-v2_060000231003b20faec8c7e38019c0d4cc02ec33b077ef3bc1e59b4a7f53fd21ec5cd455628a@finder-1689834339958814-1998268070\"><\/mp-common-videosnap><\/section>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">\u4e3b\u8981\u64cd\u4f5c\u5185\u5bb9<\/span><\/em><\/strong><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">1\u3001R\u73af\u5883\u7684\u914d\u7f6e\u4ee5\u53caR\u5305\u7684\u4e0b\u8f7d<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">R\u8bed\u8a00\u4e0b\u8f7d\u5730\u5740\uff1a<\/span><\/strong><span style=\"font-size: 14px;\">https:\/\/www.r-project.org\/<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">Rstudio<\/span><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">\u4e0b\u8f7d\u5730\u5740\uff1a<\/span><\/strong><span style=\"font-size: 14px;\">https:\/\/www.rstudio.com\/products\/rstudio\/download\/#download<\/span><\/p>\n<p style=\"white-space: normal;text-align: left;\"><strong><span style=\"font-size: 14px;\">R\u5305\u7684\u5b89\u88c5\uff1a<\/span><\/strong><span style=\"font-size: 14px;letter-spacing: 0.034em;\">ggClusterNet\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u9700\u8981\u5f88\u591a\u4f9d\u8d56\u7684\u5b89\u88c5\u5305\uff0c\u8017\u65f6\u4f1a\u4e45\u4e00\u4e9b\uff0c\u5e0c\u671b\u4f60\u8010\u5fc3\u7b49\u5f85\uff08\u5b89\u88c5\u901f\u5ea6\u53d6\u51b3\u4f60\u7684R\u73af\u5883\u4e2d\u4f9d\u8d56\u5305\u6709\u591a\u5c11\u4e2a\u4ee5\u524d\u6ca1\u6709\u4e0b\u8f7d\u8fc7\u54e6\uff5e\uff09<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5b89\u88c5<span class=\"code-snippet__function\">ggClusterNet<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__title\">devtools::install_github<\/span><span class=\"code-snippet__params\">(<span class=\"code-snippet__string\">\"taowenmicro\/ggClusterNet\"<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">2\u3001\u6784\u5efa\u6570\u636e\u683c\u5f0f<\/span><\/em><\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u52a0\u8f7d\u6240\u7528\u7684\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggClusterNet)<\/span><\/code><code><span class=\"code-snippet_outer\">library(phyloseq)<\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(igraph)<\/span><\/code><code><span class=\"code-snippet_outer\">library(sna)<\/span><\/code><code><span class=\"code-snippet_outer\">library(network)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6839\u636e\u81ea\u5df1\u7684\u6570\u636e\u683c\u5f0f\u5206\u522b\u5bfc\u5165otuable\u3001taxnomoy\u548cmetadata\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">otutable <- read.table(<span class=\"code-snippet__string\">\"table.xls\"<\/span>, header = T, sep = <span class=\"code-snippet__string\">\"t\"<\/span>,row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">taxnomoy <- read.table(<span class=\"code-snippet__string\">\"tax.txt\"<\/span>, header = T,sep = <span class=\"code-snippet__string\">\"t\"<\/span>, fill=TRUE, na.strings = <span class=\"code-snippet__string\">\"NA\"<\/span>, row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- read.table(<span class=\"code-snippet__string\">\"metadata.tsv\"<\/span>, header = T,sep = <span class=\"code-snippet__string\">\"t\"<\/span>, row.names = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6700\u540e\u5f97\u5230ps\u7684\u6570\u636e\u683c\u5f0f<\/span><\/code><code><span class=\"code-snippet_outer\">ps <- phyloseq(sample_data(metadata),otu_table(as.matrix(otutable),taxa_are_rows = T),tax_table(as.matrix(taxnomoy)))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u6784\u5efa\u597d\u540e\u53ef\u4ee5ps\u4e00\u4e0b\u770b\u4e00\u4e0b\u8fd9\u4e2a\u6570\u636e\u96c6(\u4e3b\u8981\u5305\u62ecotu_table()\u3001sample_table()\u3001tax_table()\u3001phy_table()\u56db\u4e2a\u90e8\u5206\uff09<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6570\u636e\u96c6\u7684\u6784\u5efa\u662f\u6700\u9ebb\u70e6\u7684\u5730\u65b9\u4f46\u662f\u4e00\u65e6\u6784\u5efa\u597d\uff0c\u64cd\u4f5c\u8d77\u6765\u5c31\u5f88\u65b9\u4fbf\uff0c\u5e0c\u671b\u4f60\u8010\u5fc3\u505a\u597d\u8fd9\u4e00\u6b65\uff5e<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u6784\u5efa\u597d\u6570\u636e\u683c\u5f0f\u540e\uff0c\u505a\u5171\u73b0\u7f51\u7edc\u5206\u6790\u53ea\u9700\u4e00\u884c\u4ee3\u7801\u5c31\u53ef\u4ee5\u641e\u5b9a\uff0c\u5feb\u6765\u8bd5\u4e00\u4e0b\uff5e<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">3\u3001\u4e00\u952e\u5206\u6790<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5148\u521b\u5efa\u4e00\u4e2a\u5b58\u50a8\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">path1 = <span class=\"code-snippet__string\">\".\/result_net\/\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dir.create(path1)<\/span><\/code><code><span class=\"code-snippet_outer\">result1 = network<span class=\"code-snippet__number\">.2<\/span>(ps = ps,#\u6784\u5efa\u7684\u6570\u636e\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\"> N = <span class=\"code-snippet__number\">100<\/span>, #\u53d6\u524d\u4e30\u5ea6\u6700\u9ad8\u7684\u524d<span class=\"code-snippet__number\">100<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> layout_net = <span class=\"code-snippet__string\">\"model_Gephi.2\"<\/span>, #\u5e03\u5c40\u683c\u5f0fmodel_Gephi<span class=\"code-snippet__number\">.2<\/span>\u8fd9\u91cc\u6211\u7528\u7684Gephi\u7684<\/span><\/code><code><span class=\"code-snippet_outer\"> r.threshold=<span class=\"code-snippet__number\">0.6<\/span>, #\u76f8\u5173\u6027\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"> p.threshold=<span class=\"code-snippet__number\">0.01<\/span>, #\u663e\u8457\u6027\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\"> label = TRUE, #\u662f\u5426\u5728\u8282\u70b9\u4e0a\u6807\u8bb0\u6807\u7b7e<\/span><\/code><code><span class=\"code-snippet_outer\"> path = path1, #\u5b58\u653e\u7684\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"> lab = <span class=\"code-snippet__string\">\"Genus\"<\/span>, #\u6807\u7b7e\u7528Genus \u8fd9\u91cc\u4e00\u5b9a\u8981\u4e0etaxnomoy\u4e2d\u5217\u540d\u4e00\u81f4<\/span><\/code><code><span class=\"code-snippet_outer\"> zipi = TRUE #\u662f\u5426\u7ed8\u5236zipi\u56fe)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">4\u3001\u8f93\u51fa\u6587\u4ef6\u89e3\u8bfb<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">1\u3001\u6709\u4e24\u5f20pdf\u7684\u5173\u8054\u7f51\u7edc\u56fe<span style=\"font-size: 14px;color: rgb(61, 170, 214);\">(networkXX.pdf)<\/span>\uff0c\u662f\u6839\u636e\u5305\u4e2d\u9ed8\u8ba4\u7684\u53c2\u6570\u7ed8\u5236\u7684\uff0c\u4f46\u662f\u4e00\u822c\u56fe\u5f62\u8fbe\u4e0d\u5230\u60f3\u8981\u7684\u7406\u60f3\u6548\u679c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">2\u3001\u4f1a\u8f93\u51fa\u53ef\u4ee5\u5bfc\u5165\u5230Gephi\u4e2d\u7684\u8fb9\u6587\u4ef6\u548c\u70b9\u6587\u4ef6<span style=\"font-size: 14px;color: rgb(61, 170, 214);\">\uff08XX_Gephi_edge.csv\u3001XX_Gephi_node.csv\uff09<\/span>,\u53ef\u4ee5\u5bfc\u5165\u5230Gephi\u8fdb\u884c\u8c03\u8282\u56fe\u7684\u5e03\u5c40\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: left;white-space: normal;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">5\u3001\u51fa\u7248\u7ea7\u56fe\u5f62\u89e3\u8bfb<\/span><\/em><\/strong><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u5982\u4e0b\u56fe\u5373\u4e3a\u6700\u540eGephi\u505a\u51fa\u7684\u56fe\uff1a\u6bcf\u4e2a\u8282\u70b9\u4ee3\u8868\u4e00\u4e2a\u5fae\u751f\u7269\u7684\u5c5e\u6c34\u5e73\uff0c\u989c\u8272\u4ee3\u8868\u5c5e\u6240\u5728\u7684\u95e8\u7c7b\uff0c\u5927\u5c0f\u4ee3\u8868\u5c5e\u7684\u76f8\u5bf9\u4e30\u5ea6\uff0c\u4e24\u4e2a\u5c5e\u6c34\u5e73\u4e4b\u95f4\u6b63\u76f8\u5173\u7528\u7ea2\u8272\u8fde\u63a5\uff0c\u8d1f\u76f8\u5173\u7528\u84dd\u8272\u8fde\u63a5\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_eAsqO1krcxHaDOXEV0SMgVVYBD4h0Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyL6u7wJswOp8vtpzGp6vYnKf4rIYDhaib4HWqRWFt60sKD8eAsqO1krcxHaDOXEV0SMgVVYBD4h0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">ggClusterNet\u7684\u5305\u5bf9\u5173\u8054\u7f51\u7edc\u7684\u5e03\u5c40\u4ee5\u53ca\u4e00\u4e9b\u62d3\u6251\u5b66\u6307\u6570\u7684\u8ba1\u7b97\u90fd\u5177\u6709\u76f8\u5e94\u7684\u529f\u80fd\uff0c\u5982\u679c\u60f3\u7ed8\u5236\u51fa\u6ee1\u610f\u7684\u5173\u8054\u7f51\u7edc\u56fe\uff0c\u5c31\u7528\u591a\u591a\u63a2\u7d22\uff0c\u8fd9\u91cc\u53ea\u662f\u7b80\u5355\u7684\u7ed8\u5236\u51fa\u7f51\u7edc\u56fe\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u597d\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5173\u8054\u7f51\u7edc\u56fe\u5c31\u5b8c\u6210\u4e86\u3002\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u5c31\u548c\u5c0f\u679c\u8ba8\u8bba\u5427\uff5e<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"578\" data-cropsely1=\"0\" data-cropsely2=\"322\" data-galleryid=\"\" data-ratio=\"0.7193195625759417\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_oRxs73HBHUoxCtAqBPQnq1AXricRvg-8.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxenwVZiaibuOTpj6MMDUj2LoPdS6tic40bbGQV7QyM6QOQY8EFoRxs73HBHUoxCtAqBPQnq1AXricRvg\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"823\" style=\"width: 578px;height: 416px;\" data-recalc-dims=\"1\"><\/p>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e00\u952e\u7ed8\u5236\u5fae\u751f\u7269\u5173\u8054\u7f51\u5171\u73b0\u56fe \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c &nbs […]<\/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\/59083"}],"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=59083"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59083\/revisions"}],"predecessor-version":[{"id":59087,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59083\/revisions\/59087"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59083"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59083"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59083"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}