{"id":512,"date":"2022-05-21T18:47:17","date_gmt":"2022-05-21T10:47:17","guid":{"rendered":"https:\/\/linguopeng.top\/?p=512"},"modified":"2022-05-21T18:47:18","modified_gmt":"2022-05-21T10:47:18","slug":"pca","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=512","title":{"rendered":"PCA"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>pacman::p_load(tidyverse,ggrepel,FactoMineR,magrittr,factoextra,RColorBrewer)\n\ndf &lt;- read_tsv(\"F3.xls\")\n\npca &lt;- df %>% column_to_rownames(var=\"Sample_id\") %>% \n  select(-Subtype) %>% prcomp(.,scale. = TRUE)\n\nvar_explained &lt;- pca$sdev^2\/sum(pca$sdev^2)\n\nfviz_pca_biplot(pca, axes = c(1, 2),geom.ind = c(\"point\"),geom.var = c(\"arrow\", \"text\"),\n                pointshape = 20,pointsize=4,label =\"var\",repel = TRUE,col.var = \"grey50\",\n                labelsize=0.5,\n                col.ind = df$Subtype)+\n  scale_color_manual(values = colorRampPalette(brewer.pal(12,\"Paired\"))(4))+\n  labs(x=paste0(\"(PC1: \",round(var_explained&#91;1]*100,2),\"%)\"),\n       y=paste0(\"(PC2: \",round(var_explained&#91;2]*100,2),\"%)\"),\n       title=\"PCA-Biplot\")+\n  theme(panel.background = element_rect(fill = 'white', colour = 'black'),\n        axis.title.x = element_text(colour=\"black\",size = 12,margin = margin(t=12)),\n        axis.title.y = element_text(colour=\"black\",size = 12,margin = margin(r=12)),\n        axis.text=element_text(color=\"black\"),\n        plot.title = element_text(size=12,colour = \"black\",hjust=0.5,face = \"bold\"),\n        legend.title = element_blank(),\n        legend.key=element_blank(),   # \u56fe\u4f8b\u952e\u4e3a\u7a7a\n        legend.text = element_text(color=\"black\",size=9), # \u5b9a\u4e49\u56fe\u4f8b\u6587\u672c\n        legend.spacing.x=unit(0.1,'cm'), # \u5b9a\u4e49\u6587\u672c\u4e66\u5e73\u8ddd\u79bb\n        legend.key.width=unit(0.2,'cm'), # \u5b9a\u4e49\u56fe\u4f8b\u6c34\u5e73\u5927\u5c0f\n        legend.key.height=unit(0.2,'cm'), # \u5b9a\u4e49\u56fe\u4f8b\u5782\u76f4\u5927\u5c0f\n        legend.background=element_blank(), # \u8bbe\u7f6e\u80cc\u666f\u4e3a\u7a7a\n        legend.box.background=element_rect(colour=\"black\"), # \u56fe\u4f8b\u7ed8\u5236\u8fb9\u6846\n        legend.position=c(1,0),legend.justification=c(1,0))\n<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2022\/05\/Rplot01.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"615\" height=\"475\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2022\/05\/Rplot01.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-513\"\/><\/div><\/figure>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-512","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/512","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=512"}],"version-history":[{"count":1,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/512\/revisions"}],"predecessor-version":[{"id":514,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/512\/revisions\/514"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=512"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=512"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=512"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}