{"id":57978,"date":"2024-06-16T20:58:24","date_gmt":"2024-06-16T12:58:24","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57978"},"modified":"2024-06-16T20:58:24","modified_gmt":"2024-06-16T12:58:24","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%e5%b8%a6%e4%bd%a0%e4%ba%86%e8%a7%a3r%e8%af%ad%e8%a8%80%e5%8c%85phyloseq%ef%bc%8c%e5%b8%ae%e4%bd%a0%e5%a4%84%e7%90%86%e5%a4%8d%e6%9d%82%e7%9a%84%e5%be%ae","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=57978","title":{"rendered":"\u4e24\u5206\u949f\u5e26\u4f60\u4e86\u89e3R\u8bed\u8a00\u5305\u201cphyloseq\u201d\uff0c\u5e2e\u4f60\u5904\u7406\u590d\u6742\u7684\u5fae\u751f\u7269\u7ec4\u6570\u636e"},"content":{"rendered":"


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powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(59, 149, 115);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>Phyloseq\u662f\u4e00\u4e2a\u5728\u5fae\u751f\u7269\u7ec4\u5b66\u7814\u7a76\u4e2d\u5e7f\u6cdb\u5e94\u7528\u7684R\u8bed\u8a00\u5305\u3002\u5b83\u63d0\u4f9b\u4e86\u7528\u4e8e\u5904\u7406\u3001\u5206\u6790\u548c\u53ef\u89c6\u5316\u5fae\u751f\u7269\u7ec4\u6570\u636e\u7684\u529f\u80fd\uff0c\u5305\u62ec\u5bf9\u591a\u6837\u6027\u3001\u7ec4\u6210\u548c\u7ed3\u6784\u7684\u5206\u6790\u3002Phyloseq\u7684\u8bbe\u8ba1\u76ee\u6807\u662f\u4e3a\u751f\u7269\u5b66\u5bb6\u548c\u751f\u7269\u4fe1\u606f\u5b66\u5bb6\u63d0\u4f9b\u4e00\u4e2a\u7edf\u4e00\u7684\u5de5\u5177\uff0c\u7528\u4e8e\u5904\u7406\u590d\u6742\u7684\u5fae\u751f\u7269\u7ec4\u6570\u636e\uff0c\u5e76\u8fdb\u884c\u7edf\u8ba1\u5206\u6790\u548c\u53ef\u89c6\u5316\u3002<\/p>\n<p><br \/><\/p>\n<p>\u4e0b\u9762\u662fPhyloseq\u5305\u7684\u4e00\u4e9b\u4e3b\u8981\u529f\u80fd\u548c\u7279\u70b9\uff1a<\/p>\n<p><br \/><\/p>\n<p>1. \u6570\u636e\u7ed3\u6784\uff1aPhyloseq\u5305\u901a\u8fc7\u5b9a\u4e49\u4e86\u4e00\u79cd\u65b0\u7684\u6570\u636e\u7ed3\u6784\uff08phyloseq\u5bf9\u8c61\uff09\uff0c\u5c06\u5fae\u751f\u7269\u7ec4\u6570\u636e\u7684\u5404\u4e2a\u65b9\u9762\u6574\u5408\u5728\u4e00\u8d77\u3002\u8fd9\u4e2a\u5bf9\u8c61\u5305\u542b\u4e86\u6837\u672c\u4fe1\u606f\u3001\u7269\u79cd\u6ce8\u91ca\u4fe1\u606f\u548c\u4e30\u5ea6\u6570\u636e\uff0c\u5e76\u63d0\u4f9b\u4e86\u8bb8\u591a\u7528\u4e8e\u5904\u7406\u548c\u64cd\u4f5c\u8fd9\u4e9b\u6570\u636e\u7684\u51fd\u6570\u3002<\/p>\n<p><br \/><\/p>\n<p>2. \u6570\u636e\u5904\u7406\uff1aPhyloseq\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\u7528\u4e8e\u6570\u636e\u5904\u7406\uff0c\u5305\u62ec\u6570\u636e\u8fc7\u6ee4\u3001\u8f6c\u6362\u548c\u5f52\u4e00\u5316\u3002\u4f60\u53ef\u4ee5\u6839\u636e\u9700\u6c42\u5bf9\u6837\u672c\u548c\u7269\u79cd\u8fdb\u884c\u7b5b\u9009\u3001\u6392\u5e8f\u548c\u91cd\u547d\u540d\uff0c\u4e5f\u53ef\u4ee5\u5bf9\u4e30\u5ea6\u6570\u636e\u8fdb\u884c\u5f52\u4e00\u5316\u548c\u8f6c\u6362\uff0c\u5982\u7a00\u91ca\u3001\u76f8\u5bf9\u4e30\u5ea6\u8f6c\u6362\u548c\u5bf9\u6570\u8f6c\u6362\u7b49\u3002<\/p>\n<p><br \/><\/p>\n<p>3. \u591a\u6837\u6027\u5206\u6790\uff1aPhyloseq\u5305\u62e5\u6709\u4e30\u5bcc\u7684\u591a\u6837\u6027\u5206\u6790\u529f\u80fd\uff0c\u53ef\u4ee5\u8ba1\u7b97\u548c\u6bd4\u8f83\u5404\u79cd\u591a\u6837\u6027\u6307\u6570\uff0c\u5982\u7269\u79cd\u4e30\u5bcc\u5ea6\u3001Shannon\u6307\u6570\u3001Simpson\u6307\u6570\u7b49\u3002\u5b83\u8fd8\u63d0\u4f9b\u4e86\u7528\u4e8e\u751f\u6210\u591a\u6837\u6027\u6307\u6570\u7684\u7a00\u91ca\u66f2\u7ebf\u3001\u7a00\u91ca\u8868\u548c\u7bb1\u7ebf\u56fe\u7b49\u53ef\u89c6\u5316\u5de5\u5177\u3002<\/p>\n<p><br \/><\/p>\n<p>4. \u7269\u79cd\u7ec4\u6210\u5206\u6790\uff1aPhyloseq\u53ef\u4ee5\u5e2e\u52a9\u4f60\u5206\u6790\u5fae\u751f\u7269\u7ec4\u4e2d\u7269\u79cd\u7684\u7ec4\u6210\u60c5\u51b5\u3002\u4f60\u53ef\u4ee5\u8ba1\u7b97\u7269\u79cd\u7684\u76f8\u5bf9\u4e30\u5ea6\u3001\u7ed8\u5236\u7269\u79cd\u5806\u79ef\u67f1\u72b6\u56fe\u3001\u997c\u56fe\u548c\u70ed\u56fe\u7b49\uff0c\u4ee5\u4e86\u89e3\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7269\u79cd\u7ec4\u6210\u7684\u5dee\u5f02\u3002<\/p>\n<p><br \/><\/p>\n<p>5. \u7ed3\u6784\u5206\u6790\uff1aPhyloseq\u63d0\u4f9b\u4e86\u4e00\u4e9b\u65b9\u6cd5\u7528\u4e8e\u5206\u6790\u5fae\u751f\u7269\u7ec4\u7684\u7ed3\u6784\u3002\u4f60\u53ef\u4ee5\u8fdb\u884c\u7269\u79cd\u7ec4\u6210\u7684\u975e\u5ea6\u91cf\u591a\u7ef4\u5c3a\u5ea6\u5206\u6790\uff08NMDS\uff09\u3001\u4e3b\u5750\u6807\u5206\u6790\uff08PCoA\uff09\u548c\u805a\u7c7b\u5206\u6790\uff0c\u4ee5\u63a2\u7d22\u6837\u672c\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u548c\u5dee\u5f02\u6027\u3002<\/p>\n<p><br \/><\/p>\n<p>6. \u5dee\u5f02\u4e30\u5ea6\u5206\u6790\uff1aPhyloseq\u5305\u96c6\u6210\u4e86\u4e00\u4e9b\u5e38\u7528\u7684\u5dee\u5f02\u4e30\u5ea6\u5206\u6790\u65b9\u6cd5\uff0c\u5982DESeq2\u548cedgeR\uff0c\u53ef\u4ee5\u5e2e\u52a9\u4f60\u8bc6\u522b\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u4e30\u5ea6\u5dee\u5f02\u663e\u8457\u7684\u7269\u79cd\u3002<\/p>\n<p><br \/><\/p>\n<p>7. \u53ef\u89c6\u5316\uff1aPhyloseq\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u4f7f\u4f60\u53ef\u4ee5\u4ee5\u5404\u79cd\u65b9\u5f0f\u5448\u73b0\u5fae\u751f\u7269\u7ec4\u6570\u636e\u7684\u7ed3\u679c\u3002\u4f60\u53ef\u4ee5\u7ed8\u5236\u67f1\u72b6\u56fe\u3001\u5806\u79ef\u67f1\u72b6\u56fe\u3001\u70ed\u56fe\u3001PCoA\u56fe\u548cNMDS\u56fe\u7b49\uff0c\u4ee5\u53ca\u6811\u72b6\u56fe\u548c\u7f51\u7edc\u56fe\u6765\u5c55\u793a\u3002<\/p>\n<p><br \/><\/p>\n<p>\u8981\u4f7f\u7528phyloseq\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/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=\"r\"><code><span class=\"code-snippet_outer\">> install.packages(\u201cphyloseq\u201d)  <span class=\"code-snippet__comment\"># \u5b89\u88c5phyloseq\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> library(phyloseq)  <span class=\"code-snippet__comment\"># \u52a0\u8f7dphyloseq\u5305<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u793a\u4f8b\uff1a<\/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<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=\"r\"><code><span class=\"code-snippet_outer\">> install.packages(\u201cphyloseq\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">> library(phyloseq)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u521b\u5efaOTU\u8868<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> otu_data <- matrix(<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">10<\/span>, <span class=\"code-snippet__number\">5<\/span>, <span class=\"code-snippet__number\">3<\/span>, <span class=\"code-snippet__number\">8<\/span>, <span class=\"code-snippet__number\">6<\/span>, <span class=\"code-snippet__number\">4<\/span>, <span class=\"code-snippet__number\">2<\/span>, <span class=\"code-snippet__number\">7<\/span>, <span class=\"code-snippet__number\">9<\/span>, <span class=\"code-snippet__number\">11<\/span>, <span class=\"code-snippet__number\">15<\/span>, <span class=\"code-snippet__number\">13<\/span>), nrow = <span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> rownames(otu_data) <- paste(<span class=\"code-snippet__string\">\"OTU\"<\/span>, <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">4<\/span>, sep = <span class=\"code-snippet__string\">\"\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> colnames(otu_data) <- paste(<span class=\"code-snippet__string\">\"Sample\"<\/span>, <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">3<\/span>, sep = <span class=\"code-snippet__string\">\"\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> otu_table <- otu_table(otu_data, taxa_are_rows = <span class=\"code-snippet__literal\">TRUE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u521b\u5efa\u6837\u672c\u4fe1\u606f\u8868<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> sample_data <- data.frame(<\/span><\/code><code><span class=\"code-snippet_outer\">  SampleID = paste(<span class=\"code-snippet__string\">\"Sample\"<\/span>, <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">3<\/span>, sep = <span class=\"code-snippet__string\">\"\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">  Condition = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"A\"<\/span>, <span class=\"code-snippet__string\">\"B\"<\/span>, <span class=\"code-snippet__string\">\"A\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">  stringsAsFactors = <span class=\"code-snippet__literal\">FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">)<\/span><\/code><code><span class=\"code-snippet_outer\">> rownames(sample_data) <- sample_data$SampleID<\/span><\/code><code><span class=\"code-snippet_outer\">> sample_data <- sample_data[, -<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u521b\u5efa\u7269\u79cd\u6ce8\u91ca\u8868<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> taxa_data <- data.frame(<\/span><\/code><code><span class=\"code-snippet_outer\">  OTU = paste(<span class=\"code-snippet__string\">\"OTU\"<\/span>, <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">4<\/span>, sep = <span class=\"code-snippet__string\">\"\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">  Kingdom = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Bacteria\"<\/span>, <span class=\"code-snippet__string\">\"Bacteria\"<\/span>, <span class=\"code-snippet__string\">\"Archaea\"<\/span>, <span class=\"code-snippet__string\">\"Archaea\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">  stringsAsFactors = <span class=\"code-snippet__literal\">FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">)<\/span><\/code><code><span class=\"code-snippet_outer\">> rownames(taxa_data) <- taxa_data$OTU<\/span><\/code><code><span class=\"code-snippet_outer\">> taxa_data <- taxa_data[, -<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u521b\u5efaphyloseq\u5bf9\u8c61<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> physeq <- phyloseq(otu_table, sample_data, taxa_data)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8ba1\u7b97\u7269\u79cd\u4e30\u5bcc\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> species_abundance <- transform_sample_counts(physeq, <span class=\"code-snippet__keyword\">function<\/span>(x) x \/ <span class=\"code-snippet__built_in\">sum<\/span>(x))<\/span><\/code><code><span class=\"code-snippet_outer\">> print(species_abundance)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8ba1\u7b97Shannon\u591a\u6837\u6027\u6307\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> shannon_diversity <- diversity(physeq, index = <span class=\"code-snippet__string\">\"shannon\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> print(shannon_diversity)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8ba1\u7b97Simpson\u591a\u6837\u6027\u6307\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> simpson_diversity <- diversity(physeq, index = <span class=\"code-snippet__string\">\"simpson\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> print(simpson_diversity)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u7a00\u91ca\u66f2\u7ebf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> rare_curve <- rarefy_even_depth(physeq, sample.size = <span class=\"code-snippet__number\">1000<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> plot_rarecurve(rare_curve)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.8175925925925925\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_FDx6y7GMFVSVBnDydjSUuNRdhdRpVA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaOMHVYTZsn85ksjGacWuz4WmfpFDx6y7GMFVSVBnDydjSUuNRdhdRpVA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u7269\u79cd\u5806\u79ef\u67f1\u72b6\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> plot_bar(physeq, fill = <span class=\"code-snippet__string\">\"Phylum\"<\/span>, facet_grid = ~Condition)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.8092592592592592\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ot0WuKqMuWGM2ellzMuVYGCKUm2ajA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaO4YCoOLVLicsvR7mPywicRhicBYkot0WuKqMuWGM2ellzMuVYGCKUm2ajA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u7269\u79cd\u4e30\u5ea6\u70ed\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> plot_heatmap(physeq, sample.dist = <span class=\"code-snippet__string\">\"bray\"<\/span>, tax.rank = <span class=\"code-snippet__string\">\"Phylum\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.9388888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_0bxRbk3PlwWmjbclZGCyOpLqrPZPDQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaO5Ryia9lGhlQzhvoYkfTm40TwX0bxRbk3PlwWmjbclZGCyOpLqrPZPDQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8ba1\u7b97\u6837\u672c\u4e4b\u95f4\u7684\u7269\u79cd\u7ec4\u6210\u5dee\u5f02<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> beta_div <- distance(physeq, method = <span class=\"code-snippet__string\">\"bray\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">> print(beta_div)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fdb\u884cNMDS\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> nmds <- ordinate(physeq, method = <span class=\"code-snippet__string\">\"NMDS\"<\/span>, distance = beta_div)<\/span><\/code><code><span class=\"code-snippet_outer\">> print(nmds)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236NMDS\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">> plot_ordination(physeq, nmds, color = <span class=\"code-snippet__string\">\"Condition\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9361111111111111\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_aR8oXdVOhSUexxibP8D2ZS2BNvoRcQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaOKYMNrOL8Fznuq1mAwrG0hfAYpaR8oXdVOhSUexxibP8D2ZS2BNvoRcQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" 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