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19:02:19<\/em><\/div>\n<content><\/p>\n<div class=\"topic\">\n\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3142740974448934918#wechat_redirect\" title=\"\u79d1\u7814\u4f5c\u56fe\" target=\"_blank\" rel=\"noopener\">#\u79d1\u7814\u4f5c\u56fe<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><\/p>\n<\/div>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013972\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"font-family: \u5b8b\u4f53;font-size: 15px;text-wrap: wrap;letter-spacing: 0.578px;text-align: center;\">\u5b8f\u57fa\u56e0\u7ec4\u7814\u7a76\u53ef\u4ee5\u8bf4\u662f\u751f\u4fe1\u7684\u4e00\u5927\u70ed\u95e8\u9886\u57df\uff0c\u4eca\u5929\u5c0f\u679c\u7ed9\u5927\u5bb6\u5e26\u6765\u5173\u4e8e<\/span>\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790<\/span>\u7684\u5305\u2014\u2014<\/span>ggpicrust2<\/span>\uff082023\u5e748\u6708\u65b0\u9c9c\u51fa\u7089\uff09\u3002<\/span><\/span><\/p>\n\u9884\u6d4b\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u6709\u5f88\u591a\u5de5\u5177\uff0c\u5305\u62ecPICRUSt2(Douglas et al. 2020)\u3001Tax4Fun2 (Wemheuer et al. 2020)\u3001MicFunPred (Mongad et al. 2021)\u3001PICRUSt (Langille et al. 2013)\u2026\u2026\u5728\u8fd9\u4e9b\u5de5\u5177\u91cc\u9762\uff0cPICRUSt2\u53ef\u4ee5\u8bf4\u662f\u7687\u51a0\u4e0a\u7684\u660e\u73e0\uff0c\u5b83\u520a\u767b\u5728<\/span>nature biotechnology<\/span>\u4e0a\uff08\u5c0f\u679c\u7684\u68a6\u520a\uff09\uff0c\u5df2\u7ecf\u5e2e\u52a9\u6570\u4ee5\u5343\u8ba1\u7684\u7814\u7a76\u8005\u9884\u6d4b\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u3002<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013974\" data-ratio=\"0.5677852348993289\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_nLBSibTcpNrUSuInFMTImpicZF7xJA.png?resize=560%2C317\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqQkL6w1KzBEQDicgf6NvA65CDkIRnLBSibTcpNrUSuInFMTImpicZF7xJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"745\" height=\"317 .9599609375\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe1 PICRUSt2(Douglas et al. 2020)<\/span><\/p>\n\u5de5\u5177\u867d\u597d\uff0c\u4f46\u5b66\u672f\u754c\u5bf9\u5982\u4f55\u63a8\u65ad\u5e76\u53ef\u89c6\u5316PICRUSt2\u4ea7\u751f\u7684\u529f\u80fd\u4e30\u5ea6\u8f93\u51fa\u4ecd\u7136\u6ca1\u6709\u8fbe\u6210\u5171\u8bc6\u3002\u7531\u4e8e\u4f7f\u7528\u5dee\u5f02\u4e30\u5ea6(DA)\u65b9\u6cd5\u786e\u5b9a\u7fa4\u4f53\u4e4b\u95f4\u529f\u80fd\u548c\u901a\u8def\u7684\u7edf\u8ba1\u663e\u8457\u5dee\u5f02\u662f\u5206\u6790\u4e2d\u7684\u5173\u952e\u6b65\u9aa4\uff0c\u6240\u4ee5\u5f97\u9009\u4e2a\u597d\u7684DA\u65b9\u6cd5\u3002<\/span><\/p>\nPICRUSt2\u5b98\u65b9\u6700\u521d\u63a8\u8350\u4f7f\u7528STAMP)(Parks et al. 2014)\u4f5c\u4e3a\u5206\u6790\u548c\u53ef\u89c6\u5316\u7684\u9996\u9009\u8f6f\u4ef6\u3002\u7136\u800c\uff0cSTAMP\u81ea2015\u5e74\u4ee5\u6765\u4e00\u76f4\u6ca1\u6709\u66f4\u65b0\uff0c\u6240\u4ee5\u5b83\u6ca1\u529e\u6cd5\u6574\u5408\u6700\u65b0\u7684\u6570\u636e\uff0c\u800c\u4e14\u5b83\u5728macOS\u4e0a\u5b89\u88c5\u5f88\u56f0\u96be\u3002\u4e3a\u4e86\u89e3\u51b3\u4e0a\u8ff0\u95ee\u9898\uff0cR\u8bed\u8a00\u5305ggpicrust\u6765\u4e86\uff0c\u662f\u7684\u5b83\u6765\u4e86\uff0c\u5b83\u53ef\u4ee5\u8fdb\u884c\u5e7f\u6cdb\u7684\u64e6\u4e00\u98ce\u5ea6\uff08DA\uff09\u5206\u6790\uff0c\u800c\u4e14\u63d0\u4f9b\u51fa\u7248\u7ea7\u53ef\u89c6\u5316\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nggpicrust2\u662f2023\u5e748\u67081\u65e5\u53d1\u8868\u5728<\/span>Bioinformatics<\/span>\u671f\u520a\u4e0a\uff0cgithub\u5df2\u670946\u9897\u661f\uff0c\u5c0f\u679c\u4e13\u95e8\u7ed9\u5927\u5bb6\u5206\u4eab\u65b0\u9c9c\u51fa\u7089\u7684\u5305\u54e6\uff01<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013977\" data-ratio=\"0.8334937439846006\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/3_Z3KZyUYSia2nZCEdia8EcicicCIL0w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqvTgnMCYV8b0ZeC08yDsm5KMibuwvkZ3KZyUYSia2nZCEdia8EcicicCIL0w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1039\" height=\"466.7600402832031\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe2 ggpicrust2(Chen et al. 2023)<\/span><\/p>\n\u4e0b\u9762\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u4e00\u8d77\u770b\u770b\u5982\u4f55\u4f7f\u7528ggpicrust2\u5427\uff01<\/span> <\/span><\/p>\n<section style=\"font-size: 16px;margin-bottom: 0px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n <\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/p>\n\u6587\u4ef6\u7f16\u53f7\uff1a231206<\/strong><\/em><\/span><\/p>\n\u679c\u7c89\u798f\u5229<\/span><\/strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span> <\/p>\n\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/a><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2 style=\"text-align: justify;\">\u4f7f\u7528\u65b9\u6cd5<\/span> \n <\/span><\/strong><\/span><\/h2>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013975\" data-ratio=\"1.3155021834061136\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_bXZ0RgDMibgU44RJWlbxibpcziagFA.png?resize=560%2C736\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqEMVQb7mkIHlT6qlxibF1ibRtf0BOwbXZ0RgDMibgU44RJWlbxibpcziagFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"916\" height=\"736 .6900024414062\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe3 \u5206\u6790\u6d41\u7a0b\uff08\u56fe\u6e90\uff1aChen et al. 2023\uff09<\/span><\/span><o:page><\/o:page><\/p>\n<h3 style=\"text-align: justify;\">\u73af\u5883\u51c6\u5907 \n <\/strong><\/span><\/h3>\n\u5b89\u88c5\u548c\u5176\u4ed6\u5305\u4e00\u6837\uff0c<\/span>install.packages<\/span>\u6216\u8005<\/span>install_github<\/span>\u3002<\/span><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code>install.packages(\"ggpicrust2\"<\/span>) <\/span><\/code><code># Install the devtools package if<\/span> not<\/span> already installed <\/span><\/code><code># install.packages(\"devtools\"<\/span>) <\/span><\/span><\/code><code># Install ggpicrust2 from GitHub <\/span><\/code><code>devtools::install_github(\"cafferychen777\/ggpicrust2\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u9664\u4e86\u5b89\u88c5\u5b83\u81ea\u5df1\u4ee5\u5916\u8fd8\u9700\u8981\u5b89\u88c5\u76f8\u5173\u7684\u4f9d\u8d56\u5305\u3002<\/span><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>if<\/span> (!requireNamespace(\"BiocManager\"<\/span>, quietly =TRUE<\/span>)) <\/span><\/code><code> install.packages(\"BiocManager\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>pkgs <-c(\"phyloseq\"<\/span>, \"ALDEx2\"<\/span>, \"SummarizedExperiment\"<\/span>, \"Biobase\"<\/span>, \"devtools\"<\/span>, <\/span><\/code><code> \"ComplexHeatmap\"<\/span>, \"BiocGenerics\"<\/span>, \"BiocManager\"<\/span>, \"metagenomeSeq\"<\/span>, <\/span><\/code><code> \"Maaslin2\"<\/span>, \"edgeR\"<\/span>, \"lefser\"<\/span>, \"limma\"<\/span>, \"KEGGREST\"<\/span>, \"DESeq2\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>for<\/span> (pkg in<\/span> pkgs) { <\/span><\/code><code> if<\/span> (!requireNamespace(pkg, quietly =TRUE<\/span>)) <\/span><\/code><code> BiocManager::install(pkg) <\/span><\/code><code>}<\/span><\/code><\/pre>\n<\/section>\n<h3 style=\"text-align: justify;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013976\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/5_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;color: rgb(34, 34, 38);font-family: "Times New Roman";font-size: 15px;font-weight: 700;background-color: rgb(255, 255, 255);text-align: center;\"><\/span><\/span>\u6570\u636e\u8f93\u5165 \n <\/strong><\/span><\/h3>\nggpicrust2\u5efa\u8bae\u91c7\u7528PICRUSt2\u539f\u59cb\u8f93\u51fapred_metagenome_unstrat.tsv<\/span>\u7684\u6570\u636e\u683c\u5f0f\uff0c\u4e0d\u8fc7csv\u548ctxt\u4e5f\u53ef\u4ee5\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013978\" data-ratio=\"0.5805555555555556\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_2apepRyuWt4yCAxcOrAQKZWJkzvCIQ.png?resize=560%2C325\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqyEE3DBLEeUywK703ayjT1N742apepRyuWt4yCAxcOrAQKZWJkzvCIQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"325 .260009765625\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe4 \u8f93\u5165\u6570\u636e<\/span><\/p>\n\u4e00\u4e2a\u5408\u683c\u7684\u5305\u5c31\u5f97\u63d0\u4f9b\u6837\u4f8b\u8f93\u5165\uff0c\u8fd9\u4e2a\u5305\u5f53\u7136\u4e5f\u4e0d\u4f8b\u5916\uff08\u5c0f\u679c\u5206\u4eab\u7684\u5305\u90fd\u662f\u4f18\u79c0\u7684\u597d\u5305\uff01\uff09\uff0c\u4f5c\u8005\u4e0d\u4ec5\u5728\u5305\u91cc\u63d0\u4f9b\u4e86\u6837\u4f8b\uff0c\u8fd8\u6709\u5355\u72ec\u7684\u6837\u4f8b\u6570\u636e\u6587\u4ef6\u3002\u94fe\u63a5\u5982\u4e0b\uff1a<\/span>https:\/\/drive.google.com\/drive\/folders\/1on4RKgm9NkaBCykMCCRvVJuEJeNVVqAF<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013982\" data-ratio=\"0.4137353433835846\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/7_4dUXxrr6GawlPWv9wJVGQt4wL3vUJA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqZzypyzW82sArfEMeDhJ7t51u4dUXxrr6GawlPWv9wJVGQt4wL3vUJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"597\" height=\"231.70001220703125\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe5 \u6837\u4f8b\u6570\u636e<\/span><\/p>\n\u6709\u4e24\u79cd\u6570\u636e\u5bfc\u5165\u7684\u65b9\u6cd5\uff0c\u7b2c\u4e00\u79cd\u662f\u7528\u5305\u91cc\u7684\u51fd\u6570\uff0c\u7b2c\u4e8c\u79cd\u662f\u7528\u5355\u72ec\u7684\u8bfb\u53d6\u6587\u4ef6\u51fd\u6570\uff0c\u4e24\u79cd\u90fd\u5f88\u65b9\u4fbf\uff0c\u770b\u5927\u5bb6\u4e2a\u4eba\u559c\u597d\uff0c\u6211\u8ba4\u4e3a\u7b2c\u4e8c\u79cd\u4f7f\u7528\u8303\u56f4\u66f4\u5e7f\u4e00\u4e9b\u3002<\/span><\/p>\n\u4e0b\u9762\u5c0f\u679c\u628a\u4ee3\u7801\u5949\u4e0a\uff1a<\/strong><\/span> <\/span><\/p>\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<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<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<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=\"php\"><code>library(readr) <\/span><\/code><code>library(ggpicrust2) <\/span><\/code><code>library(tibble) <\/span><\/code><code># install.packages('tidyverse') <\/span><\/span><\/code><code>library(tidyverse) <\/span><\/code><code>library(ggprism) <\/span><\/code><code>library(patchwork) <\/span><\/code><code> <\/span><\/code><code>path <-'D:\/\u5b9e\u4e60\/ggpicrust2'<\/span> <\/span><\/code><code>setwd(path) <\/span><\/code><code># \u6570\u636e\u6587\u4ef6\u4e0b\u8f7d\u5730\u5740 <\/span><\/span><\/code><code># https:\/\/drive.google.com\/drive\/folders\/1on4RKgm9NkaBCykMCCRvVJuEJeNVVqAF <\/span><\/span><\/code><code># \u52a0\u8f7d\u4e24\u4e2a\u5fc5\u987b\u7684\u6570\u636e: abundance data and metadata <\/span><\/span><\/code><code> <\/span><\/code><code># \u4ece\u6587\u4ef6\u8bfb\u53d6 <\/span><\/span><\/code><code>abundance_file <-\"abundance_file.tsv\"<\/span> <\/span><\/code><code>metadata <-read_delim( <\/span><\/code><code> \"metadata.txt\"<\/span>, <\/span><\/code><code> delim =\"t\"<\/span>, <\/span><\/code><code> escape_double =FALSE<\/span>, <\/span><\/code><code> trim_ws = TRUE<\/span> <\/span><\/code><code>) <\/span><\/code><code> <\/span><\/code><code># \u4ece\u6587\u4ef6\u540d\u5f00\u59cb <\/span><\/span><\/code><code>results_file_input <-ggpicrust2(file = abundance_file, <\/span><\/code><code> metadata = metadata, <\/span><\/code><code> group =\"Environment\"<\/span>, # For example dataset, group = \"Environment\" <\/span><\/span><\/code><code> pathway =\"KO\"<\/span>, <\/span><\/code><code> daa_method =\"LinDA\"<\/span>, <\/span><\/code><code> ko_to_kegg =TRUE<\/span>, <\/span><\/code><code> order =\"pathway_class\"<\/span>, <\/span><\/code><code> p_values_bar =TRUE<\/span>, <\/span><\/code><code> x_lab =\"pathway_name\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u770b\u7ed3\u679c <\/span><\/span><\/code><code>results_file_input[[1<\/span>]]$plot <\/span><\/code><code>results_file_input[[1<\/span>]][[1<\/span>]]$results <\/span><\/code><code> <\/span><\/code><code># \u7528\u5bfc\u8fdb\u6765\u7684\u6570\u636e\uff0cdataframe\u683c\u5f0f <\/span><\/span><\/code><code>abundance_data <-read_delim(abundance_file, delim =\"t\"<\/span>, col_names =TRUE<\/span>, trim_ws =TRUE<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u4ece\u8bfb\u8fdb\u6765\u7684\u6570\u636e\u5f00\u59cb <\/span><\/span><\/code><code>results_data_input <-ggpicrust2(data = abundance_data, <\/span><\/code><code> metadata = metadata, <\/span><\/code><code> group =\"Environment\"<\/span>, # For example dataset, group = \"Environment\" <\/span><\/span><\/code><code> pathway =\"KO\"<\/span>, <\/span><\/code><code> daa_method =\"LinDA\"<\/span>, <\/span><\/code><code> ko_to_kegg =TRUE<\/span>, <\/span><\/code><code> order =\"pathway_class\"<\/span>, <\/span><\/code><code> p_values_bar =TRUE<\/span>, <\/span><\/code><code> x_lab =\"pathway_name\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>results_data_input[[1<\/span>]]$plot <\/span><\/code><code>results_data_input[[1<\/span>]]$results<\/span><\/code><\/pre>\n<\/section>\n\u8fd9\u91cc\u7528\u5230\u4e86\u8fd9\u4e2a\u5305\u6700\u4e3b\u8981\u7684\u51fd\u6570\uff0c\u4e5f\u5c31\u662f<\/span>ggpicrust2()<\/span>\uff0c\u8fd9\u4e2a\u51fd\u6570\u7ee7\u627f\u4e86\u901a\u8def\u6ce8\u91ca\u300110\u79cd\u6700\u5148\u8fdb\u7684\u5dee\u5f02\u4e30\u5ea6\uff08DA\uff09\u65b9\u6cd5\uff0c\u4ee5\u53caDA\u7684\u53ef\u89c6\u5316\u7ed3\u679c\u3002\u4e0b\u9762\u662f\u5c0f\u679c\u4e3a\u5927\u5bb6\u6574\u7406\u7684<\/span>\u53c2\u6570\u4ecb\u7ecd<\/span>\uff1a<\/span><\/span><\/p>\n\u2022file<\/span>\uff1a\u5b57\u7b26\u4e32\uff0c\u8868\u793a\u5305\u542bKO\u4e30\u5ea6\u6570\u636e\u7684\u8f93\u5165\u6587\u4ef6\u7684\u6587\u4ef6\u8def\u5f84\uff0c\u5176\u683c\u5f0f\u7b26\u5408picrust2\u5bfc\u51fa\u683c\u5f0f\u3002\u8f93\u5165\u6587\u4ef6\u5e94\u8be5\u5728\u7b2c\u4e00\u5217\u5305\u542bKO\u6807\u8bc6\u7b26\uff0c\u5728\u7b2c\u4e00\u884c\u5305\u542b\u6837\u672c\u6807\u8bc6\u7b26\u3002\u5269\u4f59\u7684\u5355\u5143\u683c\u5e94\u8be5\u5305\u542b\u6bcf\u4e2aKO-\u6837\u672c\u5bf9\u7684\u4e30\u5ea6\u503c\u3002<\/span><\/span><\/p>\n\u2022data<\/span>\uff1adata.frame\uff0c\u4ee5\u4e0e\u8f93\u5165\u6587\u4ef6\u76f8\u540c\u7684\u683c\u5f0f\u5305\u542bKO\u4e30\u5ea6\u6570\u636e\u3002\u5982\u679c\u63d0\u4f9b\u4e86\u6b64\u53c2\u6570\uff0c\u51fd\u6570\u5c06\u4f7f\u7528\u6b64\u6570\u636e\u800c\u4e0d\u662f\u4ece\u6587\u4ef6\u4e2d\u8bfb\u53d6\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u6b64\u53c2\u6570\u8bbe\u7f6e\u4e3aNULL\u3002<\/span><\/span><\/p>\n\u2022metadata<\/span>\uff1atibble\uff0c\u5305\u542b\u6837\u672c\u4fe1\u606f\u3002<\/span><\/span><\/p>\n\u2022group<\/span>\uff1a\u5b57\u7b26\uff0c\u7ec4\u7684\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022pathway<\/span>\uff1a\u5b57\u7b26\uff0c”EC”\u3001”KO”\u6216”MetaCyc”\u4e4b\u4e00\u3002<\/span><\/span><\/p>\n\u2022daa_method<\/span>\uff1a\u5b57\u7b26\uff0c\u6307\u5b9a\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u7684\u65b9\u6cd5\uff0c\u9009\u9879\u6709\uff1a<\/span> <\/span><o:page><\/o:page><\/p>\n\u2013”ALDEx2″\uff1a\u7528\u4e8e\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u7684\u7c7b\u4f3cANOVA\u7684\u5dee\u5f02\u8868\u8fbe\u5de5\u5177\u3002<\/span><\/p>\n\u2013”DESeq2″\uff1a\u57fa\u4e8e\u8d1f\u4e8c\u9879\u5206\u5e03\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u4f7f\u7528DESeq2\u3002<\/span><\/p>\n\u2013”edgeR”\uff1a\u4f7f\u7528edgeR\u5bf9\u4e24\u7ec4\u8d1f\u4e8c\u9879\u5206\u5e03\u8ba1\u6570\u4e4b\u95f4\u7684\u5dee\u5f02\u8fdb\u884c\u7cbe\u786e\u68c0\u9a8c\u3002<\/span><\/p>\n\u2013”limma voom”\uff1aLimma-voom\u6846\u67b6\u7528\u4e8eRNA-seq\u6570\u636e\u5206\u6790\u3002<\/span><\/p>\n\u2013”metagenomeSeq”\uff1a\u4f7f\u7528metagenomeSeq\u62df\u5408\u903b\u8f91\u56de\u5f52\u6a21\u578b\uff0c\u68c0\u9a8c\u7ec4\u4e4b\u95f4\u7684\u5dee\u5f02\u4e30\u5ea6\u3002<\/span><\/p>\n\u2013”LinDA”\uff1a\u7528\u4e8e\u5fae\u751f\u7269\u7ec4\u6210\u6570\u636e\u7684\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u7684\u7ebf\u6027\u6a21\u578b\u3002<\/span><\/p>\n\u2013”Maaslin2″\uff1a\u7528\u4e8e\u591a\u53d8\u91cf\u7ebf\u6027\u6a21\u578b\u7684\u591a\u53d8\u91cf\u76f8\u5173\u6027\u5206\u6790\uff0c\u7528\u4e8e\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u3002<\/span><\/p>\n\u2022ko_to_kegg<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236KO\u4e30\u5ea6\u5230KEGG\u4e30\u5ea6\u7684\u8f6c\u6362\u3002<\/span><\/span><\/p>\n\u2022p.adjust<\/span>\uff1a\u5b57\u7b26\uff0c\u6307\u5b9ap\u503c\u8c03\u6574\u65b9\u6cd5\uff0c\u9009\u9879\u6709\uff1a<\/span><\/span><\/p>\n\u2013”BH”\uff1aBenjamini-Hochberg\u6821\u6b63\u3002<\/span><\/p>\n\u2013”holm”\uff1aHolm\u6821\u6b63\u3002<\/span><\/p>\n\u2013”bonferroni”\uff1aBonferroni\u6821\u6b63\u3002<\/span><\/p>\n\u2013”hochberg”\uff1aHochberg\u6821\u6b63\u3002<\/span><\/p>\n\u2013”fdr”\uff1aFalse discovery rate\u6821\u6b63\u3002<\/span><\/p>\n\u2013”none”\uff1a\u4e0d\u8fdb\u884cp\u503c\u6821\u6b63\u3002<\/span><\/p>\n\u2022order<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236\u4e3b\u7ed8\u56fe\u884c\u7684\u987a\u5e8f\u3002<\/span><\/span><\/p>\n\u2022p_values_bar<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236\u4e3b\u7ed8\u56fe\u662f\u5426\u5177\u6709p\u503c\u6761\u3002<\/span><\/span><\/p>\n\u2022x_lab<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236x\u8f74\u6807\u7b7e\u540d\u79f0\uff0c\u53ef\u4ece”feature”\u3001”pathway_name”\u548c”description”\u4e2d\u9009\u62e9\u3002<\/span><\/span><\/p>\n\u2022select<\/span>\uff1a\u5305\u542b\u8981\u9009\u62e9\u7684\u901a\u8def\u540d\u79f0\u7684\u5411\u91cf\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022reference<\/span>\uff1a\u5b57\u7b26\uff0c\u7528\u4e8e\u51e0\u79cdDA\u65b9\u6cd5\u7684\u53c2\u8003\u7ec4\u6c34\u5e73\u3002<\/span><\/span><\/p>\n\u2022colors<\/span>\uff1a\u4e00\u4e2a\u5305\u542b\u989c\u8272\u6570\u91cf\u7684\u5411\u91cf\u3002<\/span><\/span><\/p>\n\u4e0b\u9762\u5c31\u662fDA\u7684\u7ed3\u679c\u5566\uff0c\u5305\u542b\u4e86\u5bf9\u5e94\u901a\u8def\u7684\u76f8\u5bf9\u4e30\u5ea6\u4ee5\u53cafold change\u3002<\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013981\" data-ratio=\"0.5888888888888889\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/8_TOHiagKZm8XWYU3jic6YOQ8gcF2HfQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqqhlzJgjIfiamELjQhOicGnAbOe7mTOHiagKZm8XWYU3jic6YOQ8gcF2HfQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"329.7799987792969\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe6 DA\u7ed3\u679c<\/span><\/p>\n\u56e0\u4e3a<\/span>ggpicrust2()<\/span>\u662f\u6700\u4e3b\u8981\u7684\u51fd\u6570\uff0c\u5b83\u4e5f\u4f1a\u65f6\u4e0d\u65f6\u6709bug\uff0c\u6240\u4ee5\u4f5c\u8005\u544a\u8bc9\u6211\u4eec\uff0c\u5982\u679c\u6709\u62a5\u9519\uff0c\u53ef\u4ee5\u8bd5\u8bd5\u4e0b\u9762\u8fd9\u4e2a\u6d41\u7a0b\u3002\u5c0f\u679c\u5148\u628a\u4ee3\u7801\u8d34\u5728\u4e0b\u9762\uff1a<\/span><\/span><\/p>\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<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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code># \u52a0\u8f7dMetaCyc pathway abundance \u548c metadata <\/span><\/span><\/code><code>data(\"metacyc_abundance\"<\/span>) # \u52a0\u8f7dMetaCyc\u901a\u8def\u4e30\u5ea6\u6570\u636e <\/span><\/span><\/code><code>data(\"metadata\"<\/span>) # \u52a0\u8f7d\u5143\u6570\u636e <\/span><\/span><\/code><code># \u5982\u679c\u4f60\u6ca1\u6709\u4f7f\u7528\u793a\u4f8b\u6570\u636e\u96c6\uff0c\u8bf7\u5c06column_to_rownames()\u66f4\u6539\u4e3a\u9002\u5f53\u7684\u7279\u5f81\u5217 <\/span><\/span><\/code><code># \u5982\u679c\u4f60\u6ca1\u6709\u4f7f\u7528\u793a\u4f8b\u6570\u636e\u96c6\uff0c\u8bf7\u5c06group\u66f4\u6539\u4e3a\"\u4f60\u7684\u5206\u7ec4\u5217\u540d\" <\/span><\/span><\/code><code> <\/span><\/code><code># \u4f7f\u7528LinDA\u65b9\u6cd5 <\/span><\/span><\/code><code>metacyc_daa_results_df <-pathway_daa(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>, daa_method =\"LinDA\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u5bf9\u4e0d\u8fdb\u884cKO\u5230KEGG\u8f6c\u6362\u7684MetaCyc\u901a\u8def\u7ed3\u679c\u8fdb\u884c\u6ce8\u91ca <\/span><\/span><\/code><code>metacyc_daa_annotated_results_df <-pathway_annotation(pathway =\"MetaCyc\"<\/span>, daa_results_df = metacyc_daa_results_df, ko_to_kegg =FALSE) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8def\u8bef\u5dee\u67f1\u72b6\u56fe <\/span><\/span><\/code><code>pathway_errorbar(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), daa_results_df = metacyc_daa_annotated_results_df, Group = metadata$Environment, ko_to_kegg =FALSE, p_values_threshold =0<\/span>.05<\/span>, order =\"group\"<\/span>, select<\/span> =NULL, p_value_bar =TRUE, colors =NULL, x_lab =\"\u63cf\u8ff0\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8def\u70ed\u56fe <\/span><\/span><\/code><code># install.packages('ggh4x') <\/span><\/span><\/code><code>library(ggh4x) <\/span><\/code><code>feature_with_p_0<\/span>.05<\/span><- metacyc_daa_results_df %>%filter(p_adjust <0<\/span>.05<\/span>) <\/span><\/code><code>pathway_heatmap(abundance = metacyc_abundance %>%filter(pathway %in% feature_with_p_0<\/span>.05<\/span>$feature) %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8defPCA\u56fe <\/span><\/span><\/code><code>pathway_pca(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u5bf9\u591a\u4e2a\u65b9\u6cd5\u8fd0\u884cpathway_daa <\/span><\/span><\/code><code>methods <-c(\"ALDEx2\"<\/span>, \"DESeq2\"<\/span>, \"edgeR\"<\/span>) <\/span><\/code><code>daa_results_list <-lapply(methods, function(method) { <\/span><\/code><code> pathway_daa(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>, daa_method = method) <\/span><\/code><code>}) <\/span><\/code><code> <\/span><\/code><code># \u6bd4\u8f83\u4e0d\u540c\u65b9\u6cd5\u7684\u7ed3\u679c <\/span><\/span><\/code><code>comparison_results <-compare_daa_results(daa_results_list = daa_results_list, method_names =c(\"ALDEx2_Welch's t\u68c0\u9a8c\"<\/span>, \"ALDEx2_Wilcoxon\u79e9\u548c\u68c0\u9a8c\"<\/span>, \"DESeq2\"<\/span>, \"edgeR\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n\u8fd9\u4e9b\u51fd\u6570\u7684\u53c2\u6570\u548c<\/span>ggpicrust2()<\/span>\u7c7b\u4f3c\uff0c\u5927\u5bb6\u53ea\u8981\u5bf9\u7167\u5c0f\u679c\u524d\u6587\u7684\u53c2\u6570\u89e3\u91ca\u5373\u53ef\u3002<\/span><\/span><\/p>\nPICRUSt2\u7684\u4e3b\u6d41\u53ef\u89c6\u5316\u662fbar_plot\u3001error_bar_plot\u3001pca_plot\u3001heatmap_plot\u3002pathway_errorbar()<\/span>\u53ef\u4ee5\u663e\u793a\u7ec4\u95f4\u7684\u76f8\u5bf9\u4e30\u5ea6\u5dee\u5f02\uff0c\u4ee5\u53caDA\u7ed3\u679c\u7684log2 fold change\u548cp\u503c\u3002<\/span>pathway_pca()<\/span>\u53ef\u4ee5\u901a\u8fc7\u4e3b\u6210\u5206\u5206\u6790\u663e\u793a\u964d\u7ef4\u540e\u7684\u5dee\u5f02\u3002<\/span>pathway_heatmap()<\/span>\u53ef\u4ee5\u53ef\u89c6\u5316PICRUSt2\u8f93\u51fa\u6570\u636e\u4e2d\u7684\u6a21\u5f0f\uff0c\u8fd9\u5bf9\u4e8e\u6211\u4eec\u8bc6\u522b\u8d8b\u52bf\u6216\u7a81\u51fa\u663e\u793a\u611f\u5174\u8da3\u7684\u533a\u57df\u975e\u5e38\u6709\u7528\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013983\" data-ratio=\"0.6342592592592593\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_dGVlp2mjNLHHep1wyaSRaYp6rSiaSw.png?resize=560%2C355\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqW6WVsibRawKbMOqeEtuVt2OQANdGVlp2mjNLHHep1wyaSRaYp6rSiaSw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"355 .03997802734375\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe7 bar plot<\/span> <\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013980\" data-ratio=\"0.8363844393592678\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/10_yUODNZERVyk0GfK6dqPibcN38a9UoQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqqMzN694IEQTHwoQI3h5DFJH4UyUODNZERVyk0GfK6dqPibcN38a9UoQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"874\" height=\"468.3800048828125\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe8 \u70ed\u56fe<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013979\" data-ratio=\"0.728740581270183\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_Sjor1ickPOibgDWIicDH6pWiaCg4LQ.png?resize=560%2C408\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdq54S6keTMSjakKlSjpb91bQeLjT27Sjor1ickPOibgDWIicDH6pWiaCg4LQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"929\" height=\"408 .1000061035156\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe9 PCA\u56fe<\/span><\/p>\n<h2 style=\"text-align: justify;\">\u7ed3\u8bed<\/span><\/strong><\/span> \n <\/span><\/strong><\/h2>\n\u603b\u7ed3\u4e00\u4e0b\u3002ggpicrust2\u662f\u4e00\u4e2a\u9488\u5bf9PICRUSt2\u529f\u80fd\u9884\u6d4b\u7684\u8f93\u51fa\u6587\u4ef6\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u7684R\u5305\uff0c\u7528\u4e8e\u8fdb\u884c\u9ad8\u7ea7\u6570\u636e\u5206\u6790\u548c\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u3002ggpicrust2\u5df2\u7ecf\u88ab\u52a0\u5165\u5230PICRUSt2 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\",\"time\":\"2023-12-19 19:02:19\",\"timeStamp\":\"1702983739\"};\n<\/script> \n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497895&idx=1&sn=22cff23ab22afee1f866f1f54ec38e13&chksm=cf7f6862f808e174443b3979be9d0a608b250bcd6bf2719bf2e14427527297d12ab5ff66770e#rd\" target=\"_blank\" rel=\"noopener\">\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\">\u539f\u521b <\/span>\u5c0f\u679c <\/span><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span>2023-12-19 19:02:19<\/em><\/div>\n<content><\/p>\n<div class=\"topic\">\n\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3142740974448934918#wechat_redirect\" title=\"\u79d1\u7814\u4f5c\u56fe\" target=\"_blank\" rel=\"noopener\">#\u79d1\u7814\u4f5c\u56fe<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><\/p>\n<\/div>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013972\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"font-family: \u5b8b\u4f53;font-size: 15px;text-wrap: wrap;letter-spacing: 0.578px;text-align: center;\">\u5b8f\u57fa\u56e0\u7ec4\u7814\u7a76\u53ef\u4ee5\u8bf4\u662f\u751f\u4fe1\u7684\u4e00\u5927\u70ed\u95e8\u9886\u57df\uff0c\u4eca\u5929\u5c0f\u679c\u7ed9\u5927\u5bb6\u5e26\u6765\u5173\u4e8e<\/span>\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790<\/span>\u7684\u5305\u2014\u2014<\/span>ggpicrust2<\/span>\uff082023\u5e748\u6708\u65b0\u9c9c\u51fa\u7089\uff09\u3002<\/span><\/span><\/p>\n\u9884\u6d4b\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u6709\u5f88\u591a\u5de5\u5177\uff0c\u5305\u62ecPICRUSt2(Douglas et al. 2020)\u3001Tax4Fun2 (Wemheuer et al. 2020)\u3001MicFunPred (Mongad et al. 2021)\u3001PICRUSt (Langille et al. 2013)\u2026\u2026\u5728\u8fd9\u4e9b\u5de5\u5177\u91cc\u9762\uff0cPICRUSt2\u53ef\u4ee5\u8bf4\u662f\u7687\u51a0\u4e0a\u7684\u660e\u73e0\uff0c\u5b83\u520a\u767b\u5728<\/span>nature biotechnology<\/span>\u4e0a\uff08\u5c0f\u679c\u7684\u68a6\u520a\uff09\uff0c\u5df2\u7ecf\u5e2e\u52a9\u6570\u4ee5\u5343\u8ba1\u7684\u7814\u7a76\u8005\u9884\u6d4b\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u3002<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013974\" data-ratio=\"0.5677852348993289\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_nLBSibTcpNrUSuInFMTImpicZF7xJA.png?resize=560%2C317\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqQkL6w1KzBEQDicgf6NvA65CDkIRnLBSibTcpNrUSuInFMTImpicZF7xJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"745\" height=\"317 .9599609375\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe1 PICRUSt2(Douglas et al. 2020)<\/span><\/p>\n\u5de5\u5177\u867d\u597d\uff0c\u4f46\u5b66\u672f\u754c\u5bf9\u5982\u4f55\u63a8\u65ad\u5e76\u53ef\u89c6\u5316PICRUSt2\u4ea7\u751f\u7684\u529f\u80fd\u4e30\u5ea6\u8f93\u51fa\u4ecd\u7136\u6ca1\u6709\u8fbe\u6210\u5171\u8bc6\u3002\u7531\u4e8e\u4f7f\u7528\u5dee\u5f02\u4e30\u5ea6(DA)\u65b9\u6cd5\u786e\u5b9a\u7fa4\u4f53\u4e4b\u95f4\u529f\u80fd\u548c\u901a\u8def\u7684\u7edf\u8ba1\u663e\u8457\u5dee\u5f02\u662f\u5206\u6790\u4e2d\u7684\u5173\u952e\u6b65\u9aa4\uff0c\u6240\u4ee5\u5f97\u9009\u4e2a\u597d\u7684DA\u65b9\u6cd5\u3002<\/span><\/p>\nPICRUSt2\u5b98\u65b9\u6700\u521d\u63a8\u8350\u4f7f\u7528STAMP)(Parks et al. 2014)\u4f5c\u4e3a\u5206\u6790\u548c\u53ef\u89c6\u5316\u7684\u9996\u9009\u8f6f\u4ef6\u3002\u7136\u800c\uff0cSTAMP\u81ea2015\u5e74\u4ee5\u6765\u4e00\u76f4\u6ca1\u6709\u66f4\u65b0\uff0c\u6240\u4ee5\u5b83\u6ca1\u529e\u6cd5\u6574\u5408\u6700\u65b0\u7684\u6570\u636e\uff0c\u800c\u4e14\u5b83\u5728macOS\u4e0a\u5b89\u88c5\u5f88\u56f0\u96be\u3002\u4e3a\u4e86\u89e3\u51b3\u4e0a\u8ff0\u95ee\u9898\uff0cR\u8bed\u8a00\u5305ggpicrust\u6765\u4e86\uff0c\u662f\u7684\u5b83\u6765\u4e86\uff0c\u5b83\u53ef\u4ee5\u8fdb\u884c\u5e7f\u6cdb\u7684\u64e6\u4e00\u98ce\u5ea6\uff08DA\uff09\u5206\u6790\uff0c\u800c\u4e14\u63d0\u4f9b\u51fa\u7248\u7ea7\u53ef\u89c6\u5316\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nggpicrust2\u662f2023\u5e748\u67081\u65e5\u53d1\u8868\u5728<\/span>Bioinformatics<\/span>\u671f\u520a\u4e0a\uff0cgithub\u5df2\u670946\u9897\u661f\uff0c\u5c0f\u679c\u4e13\u95e8\u7ed9\u5927\u5bb6\u5206\u4eab\u65b0\u9c9c\u51fa\u7089\u7684\u5305\u54e6\uff01<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013977\" data-ratio=\"0.8334937439846006\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/3_Z3KZyUYSia2nZCEdia8EcicicCIL0w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqvTgnMCYV8b0ZeC08yDsm5KMibuwvkZ3KZyUYSia2nZCEdia8EcicicCIL0w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1039\" height=\"466.7600402832031\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe2 ggpicrust2(Chen et al. 2023)<\/span><\/p>\n\u4e0b\u9762\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u4e00\u8d77\u770b\u770b\u5982\u4f55\u4f7f\u7528ggpicrust2\u5427\uff01<\/span> <\/span><\/p>\n<section style=\"font-size: 16px;margin-bottom: 0px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n <\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/p>\n\u6587\u4ef6\u7f16\u53f7\uff1a231206<\/strong><\/em><\/span><\/p>\n\u679c\u7c89\u798f\u5229<\/span><\/strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span> <\/p>\n\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/a><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2 style=\"text-align: justify;\">\u4f7f\u7528\u65b9\u6cd5<\/span> \n <\/span><\/strong><\/span><\/h2>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013975\" data-ratio=\"1.3155021834061136\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_bXZ0RgDMibgU44RJWlbxibpcziagFA.png?resize=560%2C736\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqEMVQb7mkIHlT6qlxibF1ibRtf0BOwbXZ0RgDMibgU44RJWlbxibpcziagFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"916\" height=\"736 .6900024414062\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe3 \u5206\u6790\u6d41\u7a0b\uff08\u56fe\u6e90\uff1aChen et al. 2023\uff09<\/span><\/span><o:page><\/o:page><\/p>\n<h3 style=\"text-align: justify;\">\u73af\u5883\u51c6\u5907 \n <\/strong><\/span><\/h3>\n\u5b89\u88c5\u548c\u5176\u4ed6\u5305\u4e00\u6837\uff0c<\/span>install.packages<\/span>\u6216\u8005<\/span>install_github<\/span>\u3002<\/span><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code>install.packages(\"ggpicrust2\"<\/span>) <\/span><\/code><code># Install the devtools package if<\/span> not<\/span> already installed <\/span><\/code><code># install.packages(\"devtools\"<\/span>) <\/span><\/span><\/code><code># Install ggpicrust2 from GitHub <\/span><\/code><code>devtools::install_github(\"cafferychen777\/ggpicrust2\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u9664\u4e86\u5b89\u88c5\u5b83\u81ea\u5df1\u4ee5\u5916\u8fd8\u9700\u8981\u5b89\u88c5\u76f8\u5173\u7684\u4f9d\u8d56\u5305\u3002<\/span><\/span><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>if<\/span> (!requireNamespace(\"BiocManager\"<\/span>, quietly =TRUE<\/span>)) <\/span><\/code><code> install.packages(\"BiocManager\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>pkgs <-c(\"phyloseq\"<\/span>, \"ALDEx2\"<\/span>, \"SummarizedExperiment\"<\/span>, \"Biobase\"<\/span>, \"devtools\"<\/span>, <\/span><\/code><code> \"ComplexHeatmap\"<\/span>, \"BiocGenerics\"<\/span>, \"BiocManager\"<\/span>, \"metagenomeSeq\"<\/span>, <\/span><\/code><code> \"Maaslin2\"<\/span>, \"edgeR\"<\/span>, \"lefser\"<\/span>, \"limma\"<\/span>, \"KEGGREST\"<\/span>, \"DESeq2\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>for<\/span> (pkg in<\/span> pkgs) { <\/span><\/code><code> if<\/span> (!requireNamespace(pkg, quietly =TRUE<\/span>)) <\/span><\/code><code> BiocManager::install(pkg) <\/span><\/code><code>}<\/span><\/code><\/pre>\n<\/section>\n<h3 style=\"text-align: justify;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013976\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/5_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;color: rgb(34, 34, 38);font-family: "Times New Roman";font-size: 15px;font-weight: 700;background-color: rgb(255, 255, 255);text-align: center;\"><\/span><\/span>\u6570\u636e\u8f93\u5165 \n <\/strong><\/span><\/h3>\nggpicrust2\u5efa\u8bae\u91c7\u7528PICRUSt2\u539f\u59cb\u8f93\u51fapred_metagenome_unstrat.tsv<\/span>\u7684\u6570\u636e\u683c\u5f0f\uff0c\u4e0d\u8fc7csv\u548ctxt\u4e5f\u53ef\u4ee5\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013978\" data-ratio=\"0.5805555555555556\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_2apepRyuWt4yCAxcOrAQKZWJkzvCIQ.png?resize=560%2C325\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqyEE3DBLEeUywK703ayjT1N742apepRyuWt4yCAxcOrAQKZWJkzvCIQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"325 .260009765625\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe4 \u8f93\u5165\u6570\u636e<\/span><\/p>\n\u4e00\u4e2a\u5408\u683c\u7684\u5305\u5c31\u5f97\u63d0\u4f9b\u6837\u4f8b\u8f93\u5165\uff0c\u8fd9\u4e2a\u5305\u5f53\u7136\u4e5f\u4e0d\u4f8b\u5916\uff08\u5c0f\u679c\u5206\u4eab\u7684\u5305\u90fd\u662f\u4f18\u79c0\u7684\u597d\u5305\uff01\uff09\uff0c\u4f5c\u8005\u4e0d\u4ec5\u5728\u5305\u91cc\u63d0\u4f9b\u4e86\u6837\u4f8b\uff0c\u8fd8\u6709\u5355\u72ec\u7684\u6837\u4f8b\u6570\u636e\u6587\u4ef6\u3002\u94fe\u63a5\u5982\u4e0b\uff1a<\/span>https:\/\/drive.google.com\/drive\/folders\/1on4RKgm9NkaBCykMCCRvVJuEJeNVVqAF<\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013982\" data-ratio=\"0.4137353433835846\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/7_4dUXxrr6GawlPWv9wJVGQt4wL3vUJA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqZzypyzW82sArfEMeDhJ7t51u4dUXxrr6GawlPWv9wJVGQt4wL3vUJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"597\" height=\"231.70001220703125\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe5 \u6837\u4f8b\u6570\u636e<\/span><\/p>\n\u6709\u4e24\u79cd\u6570\u636e\u5bfc\u5165\u7684\u65b9\u6cd5\uff0c\u7b2c\u4e00\u79cd\u662f\u7528\u5305\u91cc\u7684\u51fd\u6570\uff0c\u7b2c\u4e8c\u79cd\u662f\u7528\u5355\u72ec\u7684\u8bfb\u53d6\u6587\u4ef6\u51fd\u6570\uff0c\u4e24\u79cd\u90fd\u5f88\u65b9\u4fbf\uff0c\u770b\u5927\u5bb6\u4e2a\u4eba\u559c\u597d\uff0c\u6211\u8ba4\u4e3a\u7b2c\u4e8c\u79cd\u4f7f\u7528\u8303\u56f4\u66f4\u5e7f\u4e00\u4e9b\u3002<\/span><\/p>\n\u4e0b\u9762\u5c0f\u679c\u628a\u4ee3\u7801\u5949\u4e0a\uff1a<\/strong><\/span> <\/span><\/p>\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<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<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<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=\"php\"><code>library(readr) <\/span><\/code><code>library(ggpicrust2) <\/span><\/code><code>library(tibble) <\/span><\/code><code># install.packages('tidyverse') <\/span><\/span><\/code><code>library(tidyverse) <\/span><\/code><code>library(ggprism) <\/span><\/code><code>library(patchwork) <\/span><\/code><code> <\/span><\/code><code>path <-'D:\/\u5b9e\u4e60\/ggpicrust2'<\/span> <\/span><\/code><code>setwd(path) <\/span><\/code><code># \u6570\u636e\u6587\u4ef6\u4e0b\u8f7d\u5730\u5740 <\/span><\/span><\/code><code># https:\/\/drive.google.com\/drive\/folders\/1on4RKgm9NkaBCykMCCRvVJuEJeNVVqAF <\/span><\/span><\/code><code># \u52a0\u8f7d\u4e24\u4e2a\u5fc5\u987b\u7684\u6570\u636e: abundance data and metadata <\/span><\/span><\/code><code> <\/span><\/code><code># \u4ece\u6587\u4ef6\u8bfb\u53d6 <\/span><\/span><\/code><code>abundance_file <-\"abundance_file.tsv\"<\/span> <\/span><\/code><code>metadata <-read_delim( <\/span><\/code><code> \"metadata.txt\"<\/span>, <\/span><\/code><code> delim =\"t\"<\/span>, <\/span><\/code><code> escape_double =FALSE<\/span>, <\/span><\/code><code> trim_ws = TRUE<\/span> <\/span><\/code><code>) <\/span><\/code><code> <\/span><\/code><code># \u4ece\u6587\u4ef6\u540d\u5f00\u59cb <\/span><\/span><\/code><code>results_file_input <-ggpicrust2(file = abundance_file, <\/span><\/code><code> metadata = metadata, <\/span><\/code><code> group =\"Environment\"<\/span>, # For example dataset, group = \"Environment\" <\/span><\/span><\/code><code> pathway =\"KO\"<\/span>, <\/span><\/code><code> daa_method =\"LinDA\"<\/span>, <\/span><\/code><code> ko_to_kegg =TRUE<\/span>, <\/span><\/code><code> order =\"pathway_class\"<\/span>, <\/span><\/code><code> p_values_bar =TRUE<\/span>, <\/span><\/code><code> x_lab =\"pathway_name\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u770b\u7ed3\u679c <\/span><\/span><\/code><code>results_file_input[[1<\/span>]]$plot <\/span><\/code><code>results_file_input[[1<\/span>]][[1<\/span>]]$results <\/span><\/code><code> <\/span><\/code><code># \u7528\u5bfc\u8fdb\u6765\u7684\u6570\u636e\uff0cdataframe\u683c\u5f0f <\/span><\/span><\/code><code>abundance_data <-read_delim(abundance_file, delim =\"t\"<\/span>, col_names =TRUE<\/span>, trim_ws =TRUE<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u4ece\u8bfb\u8fdb\u6765\u7684\u6570\u636e\u5f00\u59cb <\/span><\/span><\/code><code>results_data_input <-ggpicrust2(data = abundance_data, <\/span><\/code><code> metadata = metadata, <\/span><\/code><code> group =\"Environment\"<\/span>, # For example dataset, group = \"Environment\" <\/span><\/span><\/code><code> pathway =\"KO\"<\/span>, <\/span><\/code><code> daa_method =\"LinDA\"<\/span>, <\/span><\/code><code> ko_to_kegg =TRUE<\/span>, <\/span><\/code><code> order =\"pathway_class\"<\/span>, <\/span><\/code><code> p_values_bar =TRUE<\/span>, <\/span><\/code><code> x_lab =\"pathway_name\"<\/span>) <\/span><\/code><code> <\/span><\/code><code>results_data_input[[1<\/span>]]$plot <\/span><\/code><code>results_data_input[[1<\/span>]]$results<\/span><\/code><\/pre>\n<\/section>\n\u8fd9\u91cc\u7528\u5230\u4e86\u8fd9\u4e2a\u5305\u6700\u4e3b\u8981\u7684\u51fd\u6570\uff0c\u4e5f\u5c31\u662f<\/span>ggpicrust2()<\/span>\uff0c\u8fd9\u4e2a\u51fd\u6570\u7ee7\u627f\u4e86\u901a\u8def\u6ce8\u91ca\u300110\u79cd\u6700\u5148\u8fdb\u7684\u5dee\u5f02\u4e30\u5ea6\uff08DA\uff09\u65b9\u6cd5\uff0c\u4ee5\u53caDA\u7684\u53ef\u89c6\u5316\u7ed3\u679c\u3002\u4e0b\u9762\u662f\u5c0f\u679c\u4e3a\u5927\u5bb6\u6574\u7406\u7684<\/span>\u53c2\u6570\u4ecb\u7ecd<\/span>\uff1a<\/span><\/span><\/p>\n\u2022file<\/span>\uff1a\u5b57\u7b26\u4e32\uff0c\u8868\u793a\u5305\u542bKO\u4e30\u5ea6\u6570\u636e\u7684\u8f93\u5165\u6587\u4ef6\u7684\u6587\u4ef6\u8def\u5f84\uff0c\u5176\u683c\u5f0f\u7b26\u5408picrust2\u5bfc\u51fa\u683c\u5f0f\u3002\u8f93\u5165\u6587\u4ef6\u5e94\u8be5\u5728\u7b2c\u4e00\u5217\u5305\u542bKO\u6807\u8bc6\u7b26\uff0c\u5728\u7b2c\u4e00\u884c\u5305\u542b\u6837\u672c\u6807\u8bc6\u7b26\u3002\u5269\u4f59\u7684\u5355\u5143\u683c\u5e94\u8be5\u5305\u542b\u6bcf\u4e2aKO-\u6837\u672c\u5bf9\u7684\u4e30\u5ea6\u503c\u3002<\/span><\/span><\/p>\n\u2022data<\/span>\uff1adata.frame\uff0c\u4ee5\u4e0e\u8f93\u5165\u6587\u4ef6\u76f8\u540c\u7684\u683c\u5f0f\u5305\u542bKO\u4e30\u5ea6\u6570\u636e\u3002\u5982\u679c\u63d0\u4f9b\u4e86\u6b64\u53c2\u6570\uff0c\u51fd\u6570\u5c06\u4f7f\u7528\u6b64\u6570\u636e\u800c\u4e0d\u662f\u4ece\u6587\u4ef6\u4e2d\u8bfb\u53d6\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u6b64\u53c2\u6570\u8bbe\u7f6e\u4e3aNULL\u3002<\/span><\/span><\/p>\n\u2022metadata<\/span>\uff1atibble\uff0c\u5305\u542b\u6837\u672c\u4fe1\u606f\u3002<\/span><\/span><\/p>\n\u2022group<\/span>\uff1a\u5b57\u7b26\uff0c\u7ec4\u7684\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022pathway<\/span>\uff1a\u5b57\u7b26\uff0c”EC”\u3001”KO”\u6216”MetaCyc”\u4e4b\u4e00\u3002<\/span><\/span><\/p>\n\u2022daa_method<\/span>\uff1a\u5b57\u7b26\uff0c\u6307\u5b9a\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u7684\u65b9\u6cd5\uff0c\u9009\u9879\u6709\uff1a<\/span> <\/span><o:page><\/o:page><\/p>\n\u2013”ALDEx2″\uff1a\u7528\u4e8e\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u7684\u7c7b\u4f3cANOVA\u7684\u5dee\u5f02\u8868\u8fbe\u5de5\u5177\u3002<\/span><\/p>\n\u2013”DESeq2″\uff1a\u57fa\u4e8e\u8d1f\u4e8c\u9879\u5206\u5e03\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u4f7f\u7528DESeq2\u3002<\/span><\/p>\n\u2013”edgeR”\uff1a\u4f7f\u7528edgeR\u5bf9\u4e24\u7ec4\u8d1f\u4e8c\u9879\u5206\u5e03\u8ba1\u6570\u4e4b\u95f4\u7684\u5dee\u5f02\u8fdb\u884c\u7cbe\u786e\u68c0\u9a8c\u3002<\/span><\/p>\n\u2013”limma voom”\uff1aLimma-voom\u6846\u67b6\u7528\u4e8eRNA-seq\u6570\u636e\u5206\u6790\u3002<\/span><\/p>\n\u2013”metagenomeSeq”\uff1a\u4f7f\u7528metagenomeSeq\u62df\u5408\u903b\u8f91\u56de\u5f52\u6a21\u578b\uff0c\u68c0\u9a8c\u7ec4\u4e4b\u95f4\u7684\u5dee\u5f02\u4e30\u5ea6\u3002<\/span><\/p>\n\u2013”LinDA”\uff1a\u7528\u4e8e\u5fae\u751f\u7269\u7ec4\u6210\u6570\u636e\u7684\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u7684\u7ebf\u6027\u6a21\u578b\u3002<\/span><\/p>\n\u2013”Maaslin2″\uff1a\u7528\u4e8e\u591a\u53d8\u91cf\u7ebf\u6027\u6a21\u578b\u7684\u591a\u53d8\u91cf\u76f8\u5173\u6027\u5206\u6790\uff0c\u7528\u4e8e\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u3002<\/span><\/p>\n\u2022ko_to_kegg<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236KO\u4e30\u5ea6\u5230KEGG\u4e30\u5ea6\u7684\u8f6c\u6362\u3002<\/span><\/span><\/p>\n\u2022p.adjust<\/span>\uff1a\u5b57\u7b26\uff0c\u6307\u5b9ap\u503c\u8c03\u6574\u65b9\u6cd5\uff0c\u9009\u9879\u6709\uff1a<\/span><\/span><\/p>\n\u2013”BH”\uff1aBenjamini-Hochberg\u6821\u6b63\u3002<\/span><\/p>\n\u2013”holm”\uff1aHolm\u6821\u6b63\u3002<\/span><\/p>\n\u2013”bonferroni”\uff1aBonferroni\u6821\u6b63\u3002<\/span><\/p>\n\u2013”hochberg”\uff1aHochberg\u6821\u6b63\u3002<\/span><\/p>\n\u2013”fdr”\uff1aFalse discovery rate\u6821\u6b63\u3002<\/span><\/p>\n\u2013”none”\uff1a\u4e0d\u8fdb\u884cp\u503c\u6821\u6b63\u3002<\/span><\/p>\n\u2022order<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236\u4e3b\u7ed8\u56fe\u884c\u7684\u987a\u5e8f\u3002<\/span><\/span><\/p>\n\u2022p_values_bar<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236\u4e3b\u7ed8\u56fe\u662f\u5426\u5177\u6709p\u503c\u6761\u3002<\/span><\/span><\/p>\n\u2022x_lab<\/span>\uff1a\u5b57\u7b26\uff0c\u63a7\u5236x\u8f74\u6807\u7b7e\u540d\u79f0\uff0c\u53ef\u4ece”feature”\u3001”pathway_name”\u548c”description”\u4e2d\u9009\u62e9\u3002<\/span><\/span><\/p>\n\u2022select<\/span>\uff1a\u5305\u542b\u8981\u9009\u62e9\u7684\u901a\u8def\u540d\u79f0\u7684\u5411\u91cf\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022reference<\/span>\uff1a\u5b57\u7b26\uff0c\u7528\u4e8e\u51e0\u79cdDA\u65b9\u6cd5\u7684\u53c2\u8003\u7ec4\u6c34\u5e73\u3002<\/span><\/span><\/p>\n\u2022colors<\/span>\uff1a\u4e00\u4e2a\u5305\u542b\u989c\u8272\u6570\u91cf\u7684\u5411\u91cf\u3002<\/span><\/span><\/p>\n\u4e0b\u9762\u5c31\u662fDA\u7684\u7ed3\u679c\u5566\uff0c\u5305\u542b\u4e86\u5bf9\u5e94\u901a\u8def\u7684\u76f8\u5bf9\u4e30\u5ea6\u4ee5\u53cafold change\u3002<\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013981\" data-ratio=\"0.5888888888888889\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/8_TOHiagKZm8XWYU3jic6YOQ8gcF2HfQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqqhlzJgjIfiamELjQhOicGnAbOe7mTOHiagKZm8XWYU3jic6YOQ8gcF2HfQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"329.7799987792969\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe6 DA\u7ed3\u679c<\/span><\/p>\n\u56e0\u4e3a<\/span>ggpicrust2()<\/span>\u662f\u6700\u4e3b\u8981\u7684\u51fd\u6570\uff0c\u5b83\u4e5f\u4f1a\u65f6\u4e0d\u65f6\u6709bug\uff0c\u6240\u4ee5\u4f5c\u8005\u544a\u8bc9\u6211\u4eec\uff0c\u5982\u679c\u6709\u62a5\u9519\uff0c\u53ef\u4ee5\u8bd5\u8bd5\u4e0b\u9762\u8fd9\u4e2a\u6d41\u7a0b\u3002\u5c0f\u679c\u5148\u628a\u4ee3\u7801\u8d34\u5728\u4e0b\u9762\uff1a<\/span><\/span><\/p>\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<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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code># \u52a0\u8f7dMetaCyc pathway abundance \u548c metadata <\/span><\/span><\/code><code>data(\"metacyc_abundance\"<\/span>) # \u52a0\u8f7dMetaCyc\u901a\u8def\u4e30\u5ea6\u6570\u636e <\/span><\/span><\/code><code>data(\"metadata\"<\/span>) # \u52a0\u8f7d\u5143\u6570\u636e <\/span><\/span><\/code><code># \u5982\u679c\u4f60\u6ca1\u6709\u4f7f\u7528\u793a\u4f8b\u6570\u636e\u96c6\uff0c\u8bf7\u5c06column_to_rownames()\u66f4\u6539\u4e3a\u9002\u5f53\u7684\u7279\u5f81\u5217 <\/span><\/span><\/code><code># \u5982\u679c\u4f60\u6ca1\u6709\u4f7f\u7528\u793a\u4f8b\u6570\u636e\u96c6\uff0c\u8bf7\u5c06group\u66f4\u6539\u4e3a\"\u4f60\u7684\u5206\u7ec4\u5217\u540d\" <\/span><\/span><\/code><code> <\/span><\/code><code># \u4f7f\u7528LinDA\u65b9\u6cd5 <\/span><\/span><\/code><code>metacyc_daa_results_df <-pathway_daa(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>, daa_method =\"LinDA\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u5bf9\u4e0d\u8fdb\u884cKO\u5230KEGG\u8f6c\u6362\u7684MetaCyc\u901a\u8def\u7ed3\u679c\u8fdb\u884c\u6ce8\u91ca <\/span><\/span><\/code><code>metacyc_daa_annotated_results_df <-pathway_annotation(pathway =\"MetaCyc\"<\/span>, daa_results_df = metacyc_daa_results_df, ko_to_kegg =FALSE) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8def\u8bef\u5dee\u67f1\u72b6\u56fe <\/span><\/span><\/code><code>pathway_errorbar(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), daa_results_df = metacyc_daa_annotated_results_df, Group = metadata$Environment, ko_to_kegg =FALSE, p_values_threshold =0<\/span>.05<\/span>, order =\"group\"<\/span>, select<\/span> =NULL, p_value_bar =TRUE, colors =NULL, x_lab =\"\u63cf\u8ff0\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8def\u70ed\u56fe <\/span><\/span><\/code><code># install.packages('ggh4x') <\/span><\/span><\/code><code>library(ggh4x) <\/span><\/code><code>feature_with_p_0<\/span>.05<\/span><- metacyc_daa_results_df %>%filter(p_adjust <0<\/span>.05<\/span>) <\/span><\/code><code>pathway_heatmap(abundance = metacyc_abundance %>%filter(pathway %in% feature_with_p_0<\/span>.05<\/span>$feature) %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u751f\u6210\u901a\u8defPCA\u56fe <\/span><\/span><\/code><code>pathway_pca(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>) <\/span><\/code><code> <\/span><\/code><code># \u5bf9\u591a\u4e2a\u65b9\u6cd5\u8fd0\u884cpathway_daa <\/span><\/span><\/code><code>methods <-c(\"ALDEx2\"<\/span>, \"DESeq2\"<\/span>, \"edgeR\"<\/span>) <\/span><\/code><code>daa_results_list <-lapply(methods, function(method) { <\/span><\/code><code> pathway_daa(abundance = metacyc_abundance %>%column_to_rownames(\"pathway\"<\/span>), metadata = metadata, group =\"Environment\"<\/span>, daa_method = method) <\/span><\/code><code>}) <\/span><\/code><code> <\/span><\/code><code># \u6bd4\u8f83\u4e0d\u540c\u65b9\u6cd5\u7684\u7ed3\u679c <\/span><\/span><\/code><code>comparison_results <-compare_daa_results(daa_results_list = daa_results_list, method_names =c(\"ALDEx2_Welch's t\u68c0\u9a8c\"<\/span>, \"ALDEx2_Wilcoxon\u79e9\u548c\u68c0\u9a8c\"<\/span>, \"DESeq2\"<\/span>, \"edgeR\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n\u8fd9\u4e9b\u51fd\u6570\u7684\u53c2\u6570\u548c<\/span>ggpicrust2()<\/span>\u7c7b\u4f3c\uff0c\u5927\u5bb6\u53ea\u8981\u5bf9\u7167\u5c0f\u679c\u524d\u6587\u7684\u53c2\u6570\u89e3\u91ca\u5373\u53ef\u3002<\/span><\/span><\/p>\nPICRUSt2\u7684\u4e3b\u6d41\u53ef\u89c6\u5316\u662fbar_plot\u3001error_bar_plot\u3001pca_plot\u3001heatmap_plot\u3002pathway_errorbar()<\/span>\u53ef\u4ee5\u663e\u793a\u7ec4\u95f4\u7684\u76f8\u5bf9\u4e30\u5ea6\u5dee\u5f02\uff0c\u4ee5\u53caDA\u7ed3\u679c\u7684log2 fold change\u548cp\u503c\u3002<\/span>pathway_pca()<\/span>\u53ef\u4ee5\u901a\u8fc7\u4e3b\u6210\u5206\u5206\u6790\u663e\u793a\u964d\u7ef4\u540e\u7684\u5dee\u5f02\u3002<\/span>pathway_heatmap()<\/span>\u53ef\u4ee5\u53ef\u89c6\u5316PICRUSt2\u8f93\u51fa\u6570\u636e\u4e2d\u7684\u6a21\u5f0f\uff0c\u8fd9\u5bf9\u4e8e\u6211\u4eec\u8bc6\u522b\u8d8b\u52bf\u6216\u7a81\u51fa\u663e\u793a\u611f\u5174\u8da3\u7684\u533a\u57df\u975e\u5e38\u6709\u7528\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013983\" data-ratio=\"0.6342592592592593\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_dGVlp2mjNLHHep1wyaSRaYp6rSiaSw.png?resize=560%2C355\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqW6WVsibRawKbMOqeEtuVt2OQANdGVlp2mjNLHHep1wyaSRaYp6rSiaSw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"355 .03997802734375\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe7 bar plot<\/span> <\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013980\" data-ratio=\"0.8363844393592678\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-19_\u3010ggpicrust2\u3011\u5c0f\u679c\u6559\u4f60\u5b8f\u57fa\u56e0\u7ec4\u529f\u80fd\u9884\u6d4b\u4e0b\u6e38\u5206\u6790\/10_yUODNZERVyk0GfK6dqPibcN38a9UoQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdqqMzN694IEQTHwoQI3h5DFJH4UyUODNZERVyk0GfK6dqPibcN38a9UoQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"874\" height=\"468.3800048828125\" width=\"560.010009765625\"><\/span><\/p>\n\u56fe8 \u70ed\u56fe<\/span> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013979\" data-ratio=\"0.728740581270183\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_Sjor1ickPOibgDWIicDH6pWiaCg4LQ.png?resize=560%2C408\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyPT5Rdkc8iam7hJtPUwQPdq54S6keTMSjakKlSjpb91bQeLjT27Sjor1ickPOibgDWIicDH6pWiaCg4LQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"929\" height=\"408 .1000061035156\" width=\"560 .010009765625\" data-recalc-dims=\"1\"><\/span><\/p>\n\u56fe9 PCA\u56fe<\/span><\/p>\n<h2 style=\"text-align: justify;\">\u7ed3\u8bed<\/span><\/strong><\/span> \n <\/span><\/strong><\/h2>\n\u603b\u7ed3\u4e00\u4e0b\u3002ggpicrust2\u662f\u4e00\u4e2a\u9488\u5bf9PICRUSt2\u529f\u80fd\u9884\u6d4b\u7684\u8f93\u51fa\u6587\u4ef6\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u7684R\u5305\uff0c\u7528\u4e8e\u8fdb\u884c\u9ad8\u7ea7\u6570\u636e\u5206\u6790\u548c\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u3002ggpicrust2\u5df2\u7ecf\u88ab\u52a0\u5165\u5230PICRUSt2 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