{"id":23709,"date":"2024-01-08T17:36:06","date_gmt":"2024-01-08T09:36:06","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23709"},"modified":"2024-01-08T17:36:08","modified_gmt":"2024-01-08T09:36:08","slug":"%e5%be%ae%e7%94%9f%e7%89%a9%e7%bb%84%e4%b8%ad%e7%9a%84%e5%a4%9a%e6%a0%b7%e6%80%a7%e4%bd%a0%e6%90%9e%e6%b8%85%e6%a5%9a%e4%ba%86%e5%90%97%ef%bc%9f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23709","title":{"rendered":"\u5fae\u751f\u7269\u7ec4\u4e2d\u7684\u591a\u6837\u6027\u4f60\u641e\u6e05\u695a\u4e86\u5417\uff1f"},"content":{"rendered":"

\u751f\u6001\u5b66\u5bb6\u7528\u591a\u6837\u6027\u548c\u591a\u6837\u6027\u6765\u63cf\u8ff0\u7269\u79cd\u5728\u751f\u5883\u5185\u548c\u548c\u751f\u5883\u95f4\u7684\u591a\u6837\u6027\uff0c\u7efc\u5408\u8bc4\u4ef7\u603b\u4f53\u7684\u591a\u6837\u6027\u3002\u591a\u6837\u6027\u63cf\u8ff0\u7684\u662f\u7269\u79cd\u5185\u7684\u4e30\u5bcc\u5ea6\u3001\u591a\u6837\u6027\u3001\u5747\u5300\u5ea6\u7b49\u6307\u6807\uff0c\u56e0\u6b64\u4e5f\u88ab\u79f0\u4e3a\u751f\u5883\u5185\u591a\u6837\u6027\uff0c\u901a\u5e38\u7528\u7bb1\u7ebf\u56fe\u6765\u5c55\u73b0\u7279\u5f81\uff0c\u7528\u7a00\u758f\u66f2\u7ebf\u6837\u6765\u8bc4\u4f30\u6d4b\u5e8f\u6df1\u5ea6\u3002\u591a\u6837\u6027\u6307\u6cbf\u7740\u73af\u5883\u68af\u5ea6\u7684\u53d8\u5316\uff0c\u4e0d\u540c\u7fa4\u843d\u4e4b\u95f4\u7269\u79cd\u7ec4\u6210\u7684\u5dee\u5f02\u6027\u6216\u662f\u66f4\u66ff\u7684\u901f\u7387\uff0c\u56e0\u6b64\u4e5f\u88ab\u79f0\u4e3a\u751f\u5883\u95f4\u591a\u6837\u6027\uff0c\u901a\u7528PCoA\u56fe\u6765\u5c55\u793a\u4e0d\u540c\u6837\u6216\u8005\u7ec4\u672c\u95f4\u8ddd\u79bb\u3002<\/p>\n

\u5c0f\u679c\u4ee5\u524d\u7684\u6587\u7ae0\u66fe\u7528\u8fc7qiime2\u7684\u8fd9\u4e2a\u8f6f\u4ef6\u6765\u5f97\u5230\u7279\u5f81\u8868\u548c\u7279\u5f81\u5e8f\u5217\uff0c\u5b83\u4e0d\u4ec5\u53ef\u4ee5\u89e3\u51b3\u524d\u671f\u7684\u6570\u636e\u5904\u7406\u7684\u90e8\u5206\uff0c\u7528\u4e8e\u5206\u6790\u591a\u6837\u6027\u7684\u5206\u6790\u4e5f\u662f\u975e\u5e38\u65b9\u4fbf\u7684\u3002<\/p>\n

\u03b1\uff0c\u03b2\u591a\u6837\u6027\u6570\u636e\u5206\u6790:<\/p>\n

<\/a> 1\u3001\u53ef\u4ee5\u6253\u5305\u8f93\u51fa\u591a\u6837\u6027\u6307\u6570\uff0c\u6839\u636e\u6570\u636e\u7ed8\u5236\u7bb1\u7ebf\u56fe\u3002<\/p>\n

qiime diversity core-metrics-phylogenetic \\<\/p>\n

–i-phylogeny rooted-tree.qza \\<\/p>\n

–i-table table.qza \\<\/p>\n

–p-sampling-depth <\/a>14208\\<\/p>\n

–m-metadata-file Seed-matadata.tsv \\<\/p>\n

–output-dir core-metrics-results<\/p>\n

\u8fdb\u5316\u5173\u7cfbfaith-PD\u3001evenness\u6570\u503c\u53ef\u89c6\u5316\u3001\u9999\u6d53\u6307\u6570\u53ef\u89c6\u5316\u3001\u7269\u79cd\u6570\u76ee\u53ef\u89c6\u5316\u7b49\u53ef\u89c6\u5316\uff0cXXX\u4ee3\u8868\u6253\u5305\u8f93\u51fa\u7684\u4efb\u610f\u4e00\u79cd\u591a\u6837\u6027\u6307\u6570\u7684qza\u6587\u4ef6<\/p>\n

qiime diversity alpha-group-significance \\<\/p>\n

–i-alpha-diversity core-metrics-results\/XXX.qza \\<\/p>\n

–m-metadata-file metadata.tsv \\<\/p>\n

–o-visualization core-metrics-results\/XXX.qzv<\/p>\n

2\u3001\u4e5f\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u8981\u8ba1\u7b97\u03b1\u591a\u6837\u6027\u548c<\/a>\u03b2\u591a\u6837\u6027<\/p>\n

qiime diversity alpha-rarefaction \\<\/p>\n

–i-table <\/a>table_filtered.qza \\<\/p>\n

–i-phylogeny rooted_tree.qza \\<\/p>\n

<\/a> –p-metrics <\/a>chao1 shannon simpson observed_otus pielou_e faith_pd goods_coverage \\<\/p>\n

–p-max-depth <\/a>14208 \\<\/p>\n

–m-metadata-file map.txt<\/p>\n

–o-visualization alpha-rarefaction<\/p>\n

\u8bf4\u660e\uff1a–p-metrics\u9009\u62e9\u4e0d\u540c\u7684\u53c2\u6570<\/p>\n

<\/a> qiime diversity beta-phylogenetic \\<\/p>\n

–i-table table_filtered.qza \\<\/p>\n

–i-phylogeny rooted-tree.qza \\<\/p>\n

–p-metric [weighted_unifrac|unweighted_unifrac] \\#\u9009\u62e9\u53c2\u6570<\/p>\n

–o-distance-matrix unweighted_unifrac_distance_matrix.qza#\u8f93\u51faqza\u683c\u5f0f\u6587\u4ef6<\/p>\n

\u8bf4\u660e\uff1a\u8003\u8651\u8fdb\u5316\u5173\u7cfb<\/a>\u8ba1\u7b97\u03b2\u591a\u6837\u6027<\/p>\n

qiime diversity beta \\<\/p>\n

–i-table table.qza \\#\u8f93\u5165OTU\u8868<\/p>\n

–p-metric [correlation|sokalmichener|russellrao|hamming|rogerstanimoto|chebyshev|cityblock|kulsinski|sqeuclidean|braycurtis|yule|matching|jaccard|canberra|euclidean|seuclidean|sokalsneath|wminkowski|dice|mahalanobis|cosine]\\#\u9009\u62e9\u53c2\u6570<\/p>\n

–o-distance-matrix unweighted_unifrac_distance_matrix.qza #\u8f93\u51faqza\u683c\u5f0f\u6587\u4ef6<\/p>\n

qiime diversity core-metrics \\<\/p>\n

–i-table table_filtered.qza \\<\/p>\n

–m-metadata-file map.txt<\/p>\n

–p-sampling-depth 14208 \\<\/p>\n

–output-dir bdiv<\/p>\n

\u8bf4\u660e\uff1a\u4e0d\u8003\u8651\u8fdb\u5316\u5173\u7cfb\u8ba1\u7b97\u03b2\u591a\u6837\u6027<\/p>\n

\u4ee5\u4e0a\u6240\u6709\u8f93\u51fa\u7684\u540e\u7f00\u4e3a.qzv\u7684\u683c\u5f0f\u7684\u6587\u4ef6\u90fd\u53ef\u4ee5\u5728https:\/\/view.qiime2.org\u7f51\u7ad9\u4e0a\u62d6\u52a8\u67e5\u770b\u6570\u636e\u7684\u5206\u6790\u7ed3\u679c\uff0c\u975e\u5e38\u65b9\u4fbf\u3002\u5982\u679c\u5bf9\u4e8e\u56fe\u7247\u7684\u5c55\u793a\u7ed3\u679c\u5e76\u4e0d\u6ee1\u610f\uff0c\u53ef\u4ee5\u7528R\u8fdb\u884c\u7ed8\u56fe\u3002<\/p>\n

Aphla\u7ed8\u56fe\uff1a<\/h1>\n

\u4e00\u822c\u7528\u7bb1\u7ebf\u56fe\u6765\u5c55\u793aAphla\u7684\u7ed3\u679c\u3002<\/p>\n

df <- read.table(“.\/Shannon.txt”,header = T,sep = “\\t”)<\/p>\n

#\u8fd9\u91cc\u5904\u7406\u6570\u636e\u7684\u8fc7\u7a0b\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u60c5\u51b5\u800c\u5b9a<\/p>\n

head(df)<\/p>\n

\"\u622a\u5c4f2023-06-12<\/p>\n

p <- ggplot(df,aes(group,Chao1)) + geom_boxplot(aes(fill=group)) + theme_set(theme_bw())<\/p>\n

\"\u622a\u5c4f2023-06-12<\/p>\n

#\u7528ggplot\u7ed8\u5236\u7bb1\u7ebf\u56fe\uff0c\u5176\u5b83\u7684Aphla\u591a\u6837\u6027\u6307\u6570\u4e5f\u662f\u4e00\u6837\u7684\u7ed8\u5236\u76f8\u5e94\u7684\u56fe<\/p>\n

Beta\u591a\u6837\u6027\u6307\u6570<\/h2>\n

beta \u591a\u6837\u6027\u6307\u6570\u4e5f\u4e00\u822c\u7528PCA\u3001NMDS\u5448\u73b0\uff0c\u7528\u4e24\u7ec4\u68c0\u9a8c\u8fdb\u884c\u9a8c\u8bc1\u3002\u5728\u5c0f\u679c\u7684\u4ee5\u524d\u7684\u6587\u7ae0\u4e2d\u4e5f\u6709\u8be6\u7ec6\u7684\u8bb2\u89e3\u8fc7\u600e\u6837\u505aPCA\u56fe\uff0c\u5bf9\u4e8eNMDS\u5206\u6790\u4e5f\u53ef\u4ee5\u7528R\u4e2d\u7684venn\u5305\u5b9e\u73b0\u3002\u5177\u4f53\u7684\u64cd\u4f5c\u9700\u8981\u4e00\u7bc7\u65b0\u7684\u6587\u7ae0\u624d\u80fd\u8bb2\u5b8c\u3002<\/p>\n

\u4e0b\u56fe\u4e3aPCA\u56fe\u548cNMDS\u5c55\u793a\u7684Beta\u591a\u6837\u6027\u7684\u5206\u6790\u3002<\/p>\n

\"\u622a\u5c4f2023-06-09 \"\u622a\u5c4f2023-06-12<\/p>\n

\u901a\u8fc7qiime2\u5f3a\u5927\u7684\u6269\u589e\u5b50\u5206\u6790\u5e73\u53f0\u6211\u4eec\u4e0d\u4ec5\u53ef\u4ee5\u5904\u7406\u524d\u671f\u7684\u4e30\u5ea6\u8868\u6570\u636e\uff0c\u4e5f\u80fd\u591f\u5229\u7528\u5176\u5206\u6790\u591a\u6837\u6027\u5206\u6790\uff0c\u5e76\u80fd\u591f\u7528\u53ef\u89c6\u5316\u7ed3\u679c\u3002\u4f46\u662f\u5f80\u5f80\u653e\u5728\u8bba\u6587\u4e2d\u7684\u56fe\u7247\u90fd\u662f\u7ecf\u8fc7\u65e0\u6570\u6b21\u7684\u6253\u78e8\u7684\u3002\u56e0\u6b64\u6211\u4eec\u5728\u5f97\u5230\u6570\u636e\u7ed3\u679c\u7684\u57fa\u7840\u4e0a\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u66f4\u597d\u7684\u56fe\u5f62\u5448\u73b0\u3002\u8fd9\u4e5f\u662f\u65e0\u6570R\u5f00\u53d1\u5de5\u4f5c\u8005\u5728\u52aa\u529b\u7684\u76ee\u6807\uff0c\u4e3a\u79d1\u7814\u6dfb\u4e00\u70b9\u7f8e\u611f\uff5e<\/p>\n

\u597d\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5fae\u751f\u7269\u7ec4\u7684\u591a\u6837\u6027\u5c31\u5206\u6790\u5b8c\u6210\u4e86\u3002\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u5c31\u548c\u5c0f\u679c\u8ba8\u8bba\u5427\uff5e<\/p>\n","protected":false},"excerpt":{"rendered":"

\u751f\u6001\u5b66\u5bb6\u7528\u591a\u6837\u6027\u548c\u591a\u6837\u6027\u6765\u63cf\u8ff0\u7269\u79cd\u5728\u751f\u5883\u5185\u548c\u548c\u751f\u5883\u95f4\u7684\u591a\u6837\u6027\uff0c\u7efc\u5408\u8bc4\u4ef7\u603b\u4f53\u7684\u591a\u6837\u6027\u3002\u591a\u6837\u6027\u63cf\u8ff0\u7684\u662f\u7269\u79cd\u5185\u7684\u4e30\u5bcc […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23709"}],"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=23709"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23709\/revisions"}],"predecessor-version":[{"id":23714,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23709\/revisions\/23714"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23709"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23709"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23709"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}