{"id":305,"date":"2022-01-24T18:48:00","date_gmt":"2022-01-24T10:48:00","guid":{"rendered":"https:\/\/linguopeng.top\/?p=305"},"modified":"2022-01-24T18:48:01","modified_gmt":"2022-01-24T10:48:01","slug":"%e7%9b%b8%e5%85%b3%e6%80%a7%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=305","title":{"rendered":"\u76f8\u5173\u6027\u5206\u6790"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>library(psych)\ngenedat &lt;- read.table('index.txt', header = TRUE, sep = '\\t')\nantidat &lt;- read.table('meta.txt',header = TRUE, sep = '\\t')\n\nres &lt;- corr.test(genedat, antidat, use = 'pairwise', \n                 method = 'spearman', adjust = 'holm',\n                 alpha = 0.05)\nres$p.adj\nres$r\n\nlibrary(pheatmap)\npdat &lt;- res$r\npdat2 &lt;- matrix(ifelse(abs(pdat) &lt;= 0.3, 0, pdat), nrow(pdat))\npdat2 &lt;- matrix(ifelse(res$p.adj >= 0.05, 0, pdat2), nrow(pdat))\n\ncolnames(pdat2) &lt;- colnames(pdat)\nrownames(pdat2) &lt;- rownames(pdat)\n\nbk &lt;- seq(-1, 1, by = 0.1)\nbk\nlength(bk)\n\nmycol &lt;- c(colorRampPalette(c('blue', 'white'))(9), \n           colorRampPalette(c('white', 'white'))(3),\n           colorRampPalette(c('white', 'red'))(9))\n\npheatmap(pdat2, cellwidth = 15, cellheight = 15,\n         cluster_cols = FALSE,\n         color = mycol,\n         legend_breaks = seq(-1,1,by = 0.2),\n         breaks = bk)\n\npdat3 &lt;- data.frame(x = rep(colnames(pdat2), each = 23),\n                       y = rep(rownames(pdat2), 13),\n                       r = as.vector(res$r),\n                       p = as.vector(\n                         ifelse(res$p.adj >= 0.05, 1, res$p.adj)\n                       ))\n#########1###############\nlibrary(ggplot2)\nggplot(pdat3, aes(x,y, colour = r, size = -log10(p))) +\n  geom_point(aes(alpha = -log10(p))) + \n  scale_color_gradient2(low = 'blue',\n                        mid = 'grey',\n                        high = 'red',\n                        midpoint = 0) +\n  scale_size_area() + theme_bw() +\n  theme(axis.text.x = element_text(angle = 90))\n########################\nlibrary(readr)\ndf1&lt;-read_tsv(\"index.txt\")\nhead(df1)\ndf2&lt;-read_tsv(\"meta.txt\")\nhead(df2)\nlibrary(psych)\ncor.result&lt;-corr.test(df1,df2,method = \"pearson\")\nlibrary(tidyverse)\ncor.result$p %>% \n  as.data.frame() %>% \n  rownames_to_column() %>% \n  pivot_longer(!rowname) %>% \n  mutate(p_value=case_when(\n    value > 0.05 ~ \"A\",\n    value >0.01 &amp; value &lt;= 0.05 ~ \"B\",\n    value > 0.001 &amp; value &lt;= 0.01 ~ \"D\",\n    value &lt;= 0.001 ~ \"E\"\n  )) -> new_df1\n\nggplot()+\n  geom_tile(data=new_df1,\n            aes(x=rowname,y=name,fill=p_value))+\n  scale_fill_manual(values = c(\"white\",\"#c0c0c0\",\n                               \"#808080\",\"#3f3f3f\"))+\n  theme(legend.key = element_rect(colour=\"black\"),\n        axis.text.x = element_text(angle = 90,hjust=1,vjust=0.5))+\n  coord_equal()\ncor.result$r %>% \n  as.data.frame() %>% \n  rownames_to_column() %>% \n  pivot_longer(!rowname) %>% \n  mutate(abs_cor=abs(value)) -> new_df2\n###########2###############\nlibrary(paletteer)\nggplot()+\n # geom_tile(data=new_df1,\n  #          aes(x=rowname,y=name,fill=p_value))+\n  scale_fill_manual(values = c(\"white\",\"#c0c0c0\",\n                               \"#808080\",\"#3f3f3f\"))+\n  theme(legend.key = element_rect(colour=\"black\"),\n        axis.text.x = element_text(angle = 90,hjust=1,vjust=0.5))+\n  coord_equal()+\n  geom_point(data=new_df2,\n             aes(x=rowname,y=name,\n                 size=abs_cor,\n                 color=value))+\n  scale_color_paletteer_c(palette = \"ggthemes::Classic Red-Blue\")\n###########3###############\nggplot()+\n  geom_tile(data=new_df1,\n            aes(x=rowname,y=name,fill=p_value,alpha=p_value))+\n  scale_fill_manual(values = c(\"white\",\"#c0c0c0\",\n                               \"#808080\",\"#3f3f3f\"),\n                    label=c(\">0.05\",\n                            \"0.01~0.05\",\n                            \"0.001~0.01\",\n                            \"&lt;0.01\"))+\n  scale_alpha_manual(values = c(0,1,1,1))+\n  guides(alpha=F)+\n  theme_bw()+\n  theme(legend.key = element_rect(colour=\"black\"),\n        axis.text.x = element_text(angle = 90,\n                                   hjust=1,\n                                   vjust=0.5),)+\n  coord_equal()+\n  geom_point(data=new_df2,\n             aes(x=rowname,y=name,\n                 size=abs_cor,\n                 color=value))+\n  scale_color_paletteer_c(palette = \"ggthemes::Classic Red-Blue\")\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\/01\/Rplot-3.png'><img class=\"lazyload lazyload-style-1\" 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src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"567\" height=\"509\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2022\/01\/Rplot01-4.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-307\"\/><\/div><\/figure>\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\/Rplot02-2.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"567\" height=\"509\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2022\/01\/Rplot02-2.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-308\"\/><\/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":[3],"class_list":["post-305","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-r"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/305","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=305"}],"version-history":[{"count":1,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/305\/revisions"}],"predecessor-version":[{"id":309,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/305\/revisions\/309"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=305"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=305"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=305"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}