{"id":269,"date":"2022-01-22T15:59:17","date_gmt":"2022-01-22T07:59:17","guid":{"rendered":"https:\/\/linguopeng.top\/?p=269"},"modified":"2022-01-22T15:59:19","modified_gmt":"2022-01-22T07:59:19","slug":"%e6%a0%87%e5%bf%97%e6%98%be%e8%91%97%e6%80%a7%e7%83%ad%e5%9b%be","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=269","title":{"rendered":"\u6807\u5fd7\u663e\u8457\u6027\u70ed\u56fe"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>rm(list=ls())\r\n\r\nlibrary(pacman)\r\n\r\npacman::p_load(tidyverse,psych,reshape,ggtree,aplot)\r\n\r\n#\u5bf9genus\u8fdb\u884c\u8bfb\u53d6\uff0c\u8f6c\u7f6e\uff0c\u8f6c\u4e3a\u6570\u636e\u6846\r\n\r\ntable1 &lt;- read.delim(\"genus.xls\",header =T,sep=\"\\t\",\r\n\r\n           row.names = 1,check.names = F) %>% \r\n\r\n  t() %>% as.data.frame()\r\n\r\n#\u5bf9\u73af\u5883\u56e0\u5b50\u8fdb\u884c\u8bfb\u53d6\r\n\r\ntable2 &lt;- read.delim(\"env.xls\",header =T,sep=\"\\t\",\r\n\r\n                     row.names = 1,check.names = F)\r\n\r\n#\u5bf92\u4e2a\u6570\u636e\u5bf9\u8c61\uff0c\u76f8\u540c\u7684\u884c\u540d\uff0c\u8fdb\u884c\u8ba1\u7b97\u76f8\u5173\u6027\u53cap\u6570\u503c\u4e0e\u6821\u6b63\u3002\r\n\r\npp &lt;- corr.test(table1,table2,method=\"pearson\",adjust = \"fdr\")\r\n\r\n#\u7d22\u53d6r\u6570\u503c\u4e0ep\u6570\u503c\r\n\r\ncor &lt;- pp$r \r\n\r\npvalue &lt;- pp$p\r\n\r\n#\u5b9a\u4e49\u8ba1\u7b97\u663e\u8457\u6027\u8868\u793a\u7684\u51fd\u6570\r\n\r\nmyfun &lt;- function(pval) {\r\n\r\n  stars = \"\"\r\n\r\n  if(pval &lt;= 0.001)\r\n\r\n    stars = \"***\"\r\n\r\n  if(pval > 0.001 &amp; pval &lt;= 0.01)\r\n\r\n    stars = \"**\"\r\n\r\n  if(pval > 0.01 &amp; pval &lt;= 0.05)\r\n\r\n    stars = \"*\"\r\n\r\n  if(pval > 0.05 &amp; pval &lt;= 0.1)\r\n\r\n    stars = \"\"\r\n\r\n  stars\r\n\r\n}\r\n\r\n#melt\u51fd\u6570\u5c06\u5bbd\u8868\u8f6c\u4e3a\u957f\u8868\uff0crename\u8bbe\u7f6e\u5217\u540d\uff0cmutate\u51fd\u6570\u9009\u53d6\u6574\u5217\uff0c\u8ba1\u7b97\uff0c\u6dfb\u52a0\u5217\u3002\r\n\r\nheatmap &lt;- melt(cor) %>% rename(replace=c(\"X1\"=\"sample\",\"X2\"=\"gene\",\r\n\r\n                                          \"value\"=\"cor\")) %>%\r\n\r\n  mutate(pvalue=melt(pvalue)&#91;,3]) %>%\r\n\r\n  mutate(signif = sapply(pvalue, function(x) myfun(x)))\r\n\r\n\r\n\r\nwrite.table (heatmap,file =\"heatmap.xls\", sep =\"\\t\", row.names = F)\r\n\r\n#\u5bf9cor\u7684\u8ddd\u79bb\u77e9\u9635\u8fdb\u884c\u805a\u7c7b\r\n\r\nphr &lt;- hclust(dist(cor)) %>% \r\n\r\n  ggtree(layout=\"rectangular\", branch.length=\"none\")\r\n\r\n#\u5bf9\u5217cor\u7684\u8ddd\u79bb\u77e9\u9635\u8fdb\u884c\u805a\u7c7b\r\n\r\nphc &lt;- hclust(dist(t(cor))) %>% ggtree() + layout_dendrogram()\r\n\r\n#\u5bf9cor\u7684\u6570\u503c\u8fdb\u884c\u753b\u70ed\u56fe\r\n\r\npp &lt;- ggplot(heatmap,aes(gene,sample,fill=cor)) + \r\n\r\n  geom_tile()+theme_minimal()+\r\n\r\n  scale_fill_viridis_c()+\r\n\r\n  geom_text(aes(label=signif),size=5,color=\"white\",hjust=0.5,vjust=0.5)+\r\n\r\n  scale_y_discrete(position=\"right\")+xlab(NULL) + ylab(NULL)+\r\n\r\n  theme(axis.text.x=element_text(angle =90,hjust=1,vjust=0.5,\r\n\r\n                                 family = \"Times\",face = \"italic\",colour = \"black\",size=12),\r\n\r\n        axis.text.y=element_text(family= \"Times\",\r\n\r\n                                 face = \"plain\",colour = \"black\",size=12),\r\n\r\n        legend.text=element_text(face=\"plain\",family = \"Times\",\r\n\r\n                                 colour = \"black\",size = 12))+\r\n\r\n  guides(fill = guide_colorbar(direction = \"vertical\",reverse = F, \r\n\r\n                               barwidth = unit(.5, \"cm\"),\r\n\r\n                               barheight = unit(8, \"cm\")))+labs(fill= \"\")\r\n\r\n#\u70ed\u56fe\u4e0e\u805a\u7c7b\u56fe\u7ed3\u5408\u5728\u4e00\u8d77\r\n\r\npp %>% insert_left(phr, width=.2) %>%\r\n\r\n  insert_top(phc, height=.1)<\/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\/01\/QQ\u6d4f\u89c8\u5668\u622a\u56fe20220122155614.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"615\" height=\"469\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2022\/01\/QQ\u6d4f\u89c8\u5668\u622a\u56fe20220122155614.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-270\"\/><\/div><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\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-269","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/269","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=269"}],"version-history":[{"count":1,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/269\/revisions"}],"predecessor-version":[{"id":271,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/269\/revisions\/271"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=269"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=269"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=269"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}