{"id":60,"date":"2021-10-18T00:38:50","date_gmt":"2021-10-17T16:38:50","guid":{"rendered":"https:\/\/linguopeng.top\/?p=60"},"modified":"2021-10-18T00:38:52","modified_gmt":"2021-10-17T16:38:52","slug":"lefse","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=60","title":{"rendered":"lefse"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">##\u5bf9\u5e94\u4e8e\u4e0a\u8ff0 A-F 6 \u4e2a\u6a21\u5757\uff0c\u672c\u5730\u7248\u7684\u547d\u4ee4\u884c\u64cd\u4f5c\u793a\u4f8b\u5982\u4e0b\uff0c\u6211\u7684\u7f51\u76d8\/\u535a\u5ba2\u7d20\u6750\/lefse<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#A\uff0c\u8bbe\u7f6e LEfSe \u7684\u6570\u636e\u683c\u5f0f\uff0c\u8be6\u60c5 format_input.py -h<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#-c\uff0c\u6307\u5b9a class \u7684\u884c\uff08\u5fc5\u987b\u6307\u5b9a\uff09\uff1b-s\uff0c\u6307\u5b9a sub_class \u7684\u884c\uff08\u53ef\u7f3a\u7701\uff09\uff1b<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#-u\uff0c\u6307\u5b9a subject_id \u7684\u884c\uff08\u53ef\u7f3a\u7701\uff09\uff1b-o\uff0c\u8bbe\u7f6e\u5f52\u4e00\u5316\u503c\uff0c\u9ed8\u8ba4 -1 \u5373\u4e0d\u6267\u884c\u6807\u51c6\u5316<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#\u6ce8\uff1a\u7248\u672c\u95ee\u9898\uff0c\u6709\u65f6 format_input.py \u547d\u4ee4\u627e\u4e0d\u5230\uff0c\u53ef\u80fd\u4e3a lefse-format_input.py<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#python format_input.py lefse_test.txt A_lefse_test.in -c 1 -s 2 -u 3 -o 1000000<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>format_input.py lefse_test.txt A_lefse_test.in -c 1 -s 2 -u 3 -o 1000000`<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">#B\uff0cLEfSe \u5206\u6790\uff0c\u8be6\u60c5 run_lefse.py -h<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#-l 2.0\uff0c\u8bbe\u5b9a LDA \u5f97\u5206\u7684\u5bf9\u6570\u503c\u7684\u6700\u4f4e\u9608\u503c\u4e3a 2<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>run_lefse.py A_lefse_test.in B_lefse_test.res -l 2.0<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/1-4.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"795\" height=\"821\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/1-4.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-61\"\/><\/div><\/figure>\n\n\n\n<pre class=\"wp-block-code\"><code>run_lefse.py A_lefse_test.in B_lefse_test.res -l 4.0<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/2-1.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"775\" height=\"483\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/2-1.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-62\"\/><\/div><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">#\u5907\u6ce8\uff1a\u5bf9\u4e8e B \u7684\u8f93\u51fa\uff0c\u6211\u4eec\u53ef\u4ee5\u9009\u62e9\u4ece\u4e2d\u5220\u4e00\u4e9b\u4e0d\u5fc5\u8981\uff08\u4e0d\u663e\u8457\uff09\u7684\u6570\u636e\uff0c<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#\u4ee5\u589e\u5f3a C\u3001D\u3001E \u4f5c\u56fe\u65f6\u7684\u7f8e\u611f<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#C\uff0c\u7ed8\u5236 LEfSe \u5f97\u5206\u503c\uff0c\u8be6\u60c5 plot_res.py -h<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#\u6ce8\uff1a\u7248\u672c\u95ee\u9898\uff0c\u6709\u65f6 plot_res.py \u547d\u4ee4\u627e\u4e0d\u5230\uff0c\u53ef\u80fd\u4e3a lefse-plot_res.py<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#lefse-plot_res.py B_lefse_test.res C_lefse_test.lda.pdf &#8211;format pdf &#8211;dpi 150 &#8211;width 16<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>plot_res.py B_lefse_test.res C_lefse_test.lda.pdf --format pdf --dpi 150 --width 16<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">#D\uff0c\u7ed8\u5236\u8fdb\u5316\u5206\u652f\u56fe\uff0c\u8be6\u60c5 plot_cladogram.py -h<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#\u6ce8\uff1a\u7248\u672c\u95ee\u9898\uff0c\u6709\u65f6 plot_cladogram.py \u547d\u4ee4\u627e\u4e0d\u5230\uff0c\u53ef\u80fd\u4e3a lefse-plot_cladogram.py<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code> plot_cladogram.py B_lefse_test.res D_lefse_test.cladogram.pdf --format pdf --dpi 150<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/3-1.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"811\" height=\"572\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/3-1.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-63\"\/><\/div><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/4-1.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"833\" height=\"549\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/4-1.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-64\"\/><\/div><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">#E\uff0c\u5355\u5f20\u56fe\u7684\u5c55\u793a\u7565\uff0c\u76f4\u63a5\u4f7f\u7528 F \u7ed8\u5236\u6240\u6709\u7684\u56fe<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#F\uff0c\u7ed8\u5236\u5dee\u5f02\u7279\u5f81\uff0c\u8be6\u60c5 plot_features.py -h<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">#\u6ce8\uff1a\u7248\u672c\u95ee\u9898\uff0c\u6709\u65f6 plot_features.py \u547d\u4ee4\u627e\u4e0d\u5230\uff0c\u53ef\u80fd\u4e3a lefse-plot_features.py<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>mkdir -p F_out\nplot_features.py A_lefse_test.in B_lefse_test.res F_out\/lefse_test --format pdf --dpi 200<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>##\u5bf9\u5e94\u4e8e\u4e0a\u8ff0 A-F 6 \u4e2a\u6a21\u5757\uff0c\u672c\u5730\u7248\u7684\u547d\u4ee4\u884c\u64cd\u4f5c\u793a\u4f8b\u5982\u4e0b\uff0c\u6211\u7684\u7f51\u76d8\/\u535a\u5ba2\u7d20\u6750\/lefse #A\uff0c\u8bbe\u7f6e L [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9],"tags":[10],"class_list":["post-60","post","type-post","status-publish","format-standard","hentry","category-linux","tag-10"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/60","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=60"}],"version-history":[{"count":1,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/60\/revisions"}],"predecessor-version":[{"id":65,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/60\/revisions\/65"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=60"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=60"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=60"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}