{"id":25872,"date":"2024-01-23T17:36:43","date_gmt":"2024-01-23T09:36:43","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25872"},"modified":"2024-01-23T17:36:44","modified_gmt":"2024-01-23T09:36:44","slug":"%e5%8d%81%e5%88%86%e9%92%9f%e5%ae%9e%e7%8e%b0kegg%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%e5%a4%9a%e5%85%83%e5%8f%af%e8%a7%86%e5%8c%96","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25872","title":{"rendered":"\u5341\u5206\u949f\u5b9e\u73b0KEGG\u5bcc\u96c6\u5206\u6790\u591a\u5143\u53ef\u89c6\u5316"},"content":{"rendered":"

<\/h1>\n

\u539f\u7406\u7b80\u4ecb<\/h2>\n

KEGG\u5bcc\u96c6\u5206\u6790\u662f\u4e00\u79cd\u751f\u7269\u4fe1\u606f\u5b66\u65b9\u6cd5\uff0c\u7528\u4e8e\u89e3\u91ca\u548c\u7406\u89e3\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u7684\u529f\u80fd\u548c\u53c2\u4e0e\u7684\u4ee3\u8c22\u901a\u8def\u3002\u8be5\u5206\u6790\u4f7f\u7528KEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u6570\u636e\u5e93\u4e2d\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u5c06\u7814\u7a76\u4e2d\u53d1\u73b0\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u4e0e\u5df2\u77e5\u7684\u4ee3\u8c22\u901a\u8def\u548c\u529f\u80fd\u8fdb\u884c\u5173\u8054\u3002<\/p>\n

KEGG\u5bcc\u96c6\u5206\u6790\u901a\u5e38\u5305\u62ec\u4ee5\u4e0b\u6b65\u9aa4\uff1a1\u3001\u5c06\u611f\u5174\u8da3\u7684\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u5217\u8868\u4e0eKEGG\u6570\u636e\u5e93\u4e2d\u7684\u57fa\u56e0ID\u6216\u8def\u5f84way ID\u8fdb\u884c\u6bd4\u5bf9\u30022\u3001\u4f7f\u7528\u7edf\u8ba1\u65b9\u6cd5\uff0c\u5982Fisher\u7cbe\u786e\u68c0\u9a8c\u6216\u8d85\u51e0\u4f55\u5206\u5e03\u6cd5\uff0c\u8ba1\u7b97\u5728\u7ed9\u5b9a\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u5217\u8868\u73b0\u7279\u5b9a\u4ee3\u8c22\u901a\u8def\u6216\u529f\u80fd\u7684\u663e\u8457\u6027\u30023\u3001\u6839\u636e\u663e\u8457\u6027\u6c34\u5e73\u5bf9\u7ed3\u679c\u8fdb\u884c\u7b5b\u9009\uff0c\u786e\u5b9a\u5177\u6709\u751f\u7269\u5b66\u610f\u4e49\u7684\u901a\u8def\u6216\u529f\u80fd\u30024\u3001\u901a\u8fc7KEGG\u5bcc\u96c6\u5206\u6790\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u8bc6\u522b\u4e0e\u7814\u7a76\u5bf9\u8c61\u76f8\u5173\u8054\u7684\u4ee3\u8c22\u901a\u8def\u3001\u4fe1\u53f7\u901a\u8def\u548c\u529f\u80fd\u6a21\u5757\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u5728\u751f\u7269\u4f53\u5185\u7684\u4f5c\u7528\u548c\u8c03\u63a7\u3002<\/p>\n

\u4eca\u5929\u5c0f\u679c\u5e26\u5927\u5bb6\u5b9e\u73b0KEGG\u7684\u5bcc\u96c6\u5206\u6790\uff5e<\/p>\n

\u4ee3\u7801\u5b9e\u73b0<\/h2>\n

\u8bfb\u5165\u4e00\u4e2a\u793a\u4f8b\u6570\u636e<\/h3>\n

data <- read.delim(“Downloads\/kegg_rich.txt”,header = T,na.strings = T)<\/p>\n

#\u52a0\u8f7d\u76f8\u5e94\u7684\u8f6f\u4ef6\u5305<\/p>\n

library(tidyverse)<\/p>\n

colnames(data)<\/p>\n

data_1<-subset(data,p.adjust<0.05)<\/p>\n

colnames(data_1)<\/p>\n

\"\u622a\u5c4f2023-07-19<\/p>\n

\u8fd8\u8bb0\u5f97\u5c0f\u679c\u5728\u8bb2R\u8bed\u8a00\u7684\u989c\u8272\u7684\u65f6\u5019\u7ed9\u5927\u5bb6\u5206\u4eab\u7684paletteer\u5305\u561b\uff0c\u8fd9\u91cc\u53ef\u4ee5\u5e94\u7528\u4e00\u4e0b\u5566\uff5e<\/p>\n

\u6dfb\u52a0\u81ea\u5b9a\u4e49\u914d\u8272\u65b9\u6848\uff1a<\/h3>\n

library(paletteer)#\u914d\u8272\u5305<\/p>\n

d_palettes <- palettes_d_names<\/p>\n

paletteer_d(“ggthemes::wsj_dem_rep”,n=3)<\/p>\n

col_bar1<-paletteer_d(“ggthemes::wsj_dem_rep”,n=3)<\/p>\n

col_bar1<\/p>\n

\"\u622a\u5c4f2023-07-19<\/p>\n

\u753b\u56fe<\/h3>\n

\u6392\u5e8f\u67f1\u72b6\u56fe<\/h4>\n

\u7b80\u5355\u7ed8\u5236\uff1a<\/p>\n

ggplot(data_1)+<\/p>\n

geom_col(aes(x=Count,y=reorder(Description,Count),fill=pvalue),color=’black’,width = 0.6)<\/p>\n

\"\u622a\u5c4f2023-07-19<\/p>\n

\u6dfb\u52a0count\u3001\u989c\u8272\u3001\u548c\u4e3b\u9898<\/p>\n

ggplot(data_1)+<\/p>\n

geom_col(aes(x=Count,y=reorder(Description,Count),fill=pvalue),color=’black’,width = 0.6)+<\/p>\n

geom_text(aes(x=Count,y=reorder(Description,Count),label =Count),hjust=-0.5,vjust =0.5)+<\/p>\n

scale_fill_gradientn(colours = c(‘#B1283AFF’,’#006A8EFF’))+<\/p>\n

theme_minimal()+<\/p>\n

scale_y_discrete(expand = c(0,0))+<\/p>\n

geom_vline(xintercept = 0,lwd=0.1,color=”black”)+<\/p>\n

theme(legend.position = ‘right’)+ylab(NULL)<\/p>\n

\"\u622a\u5c4f2023-07-19<\/p>\n

\u5bcc\u96c6\u6c14\u6ce1\u56fe<\/h4>\n

ggplot(data_1)+<\/p>\n

geom_point(aes(x=Count,y=Description,color=pvalue,size=Count))+<\/p>\n

scale_color_gradientn(colours = c(‘red’,’green’))+<\/p>\n

theme_test()+<\/p>\n

ylab(NULL)<\/p>\n

\"\u622a\u5c4f2023-07-19<\/h3>\n

3\u3001\u5e26\u6709\u6807\u7b7e\u7684\u6c14\u6ce1\u56fe<\/h4>\n

\u5229\u7528ggrepel\u4e2d\u7684geom_label_repel\u51fd\u6570<\/p>\n

#\u53d6\u4e00\u4e2a-log10\u53d8\u6210\u4e00\u5217<\/p>\n

data_1$logP<- -log10(data_1$pvalue)<\/p>\n

library(ggrepel)<\/p>\n

col_bar2<-paletteer_d(“ggsci::default_igv”,n=50) #\u53bb\u53e6\u5916\u4e00\u4e2a\u8272\u5757\u7684\u989c\u8272<\/p>\n

col_bar2<\/p>\n

colnames(data_1) \"\u622a\u5c4f2023-07-19<\/p>\n

ggplot(data_1)+<\/p>\n

geom_point(aes(x=logP,y=Description,size=Count,color=Description))+<\/p>\n

scale_color_manual(values = col_bar2)+<\/p>\n

theme_test()+<\/p>\n

guides(color=F)+<\/p>\n

geom_label_repel(aes(x=logP,y=Description,label=Description),<\/p>\n

size=4,nudge_y = 0.1)+<\/p>\n

theme(axis.text.y = element_blank(),<\/p>\n

axis.ticks.y = element_blank())+<\/p>\n

xlim(c(min(data_1$logP)-2,max(data_1$logP)+2))+<\/p>\n

xlab(bquote(-Log[10] ~ italic(‘Pvalue’)))+ylab(bquote(italic(‘KEGG Pathway’)))<\/p>\n

\"\u622a\u5c4f2023-07-19<\/p>\n

KEGG\u5bcc\u96c6\u5206\u6790\u4f5c\u7528<\/h3>\n

\u529f\u80fd\u6ce8\u91ca\u548c\u89e3\u91ca\uff1aKEGG\u6570\u636e\u5e93\u63d0\u4f9b\u4e86\u8be6\u7ec6\u7684\u751f\u7269\u901a\u8def\u548c\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\uff0c\u901a\u8fc7KEGG\u5bcc\u96c6\u5206\u6790\u53ef\u4ee5\u786e\u5b9a\u57fa\u56e0\u96c6\u5408\u4e0e\u54ea\u4e9b\u751f\u7269\u5b66\u529f\u80fd\u3001\u4fe1\u53f7\u901a\u8def\u6216\u5316\u5b66\u53cd\u5e94\u76f8\u5173\u8054\u3002\u8fd9\u6709\u52a9\u4e8e\u7814\u7a76\u4eba\u5458\u7406\u89e3\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\u7684\u5173\u952e\u751f\u7269\u8fc7\u7a0b\u548c\u8c03\u63a7\u673a\u5236\u3002<\/p>\n

1\u3001\u751f\u7269\u6807\u5fd7\u7269\u9274\u5b9a\uff1a\u901a\u8fc7\u6bd4\u8f83\u4e0d\u540c\u5b9e\u9a8c\u7ec4\u4e4b\u95f4\u57fa\u56e0\u8868\u8fbe\u5dee\u5f02\uff0c\u5728\u7279\u5b9a\u75be\u75c5\u72b6\u6001\u4e0b\u5bf9\u57fa\u56e0\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u53ef\u4ee5\u5e2e\u52a9\u9274\u5b9a\u4e0e\u8be5\u75be\u75c5\u76f8\u5173\u7684\u751f\u7269\u6807\u5fd7\u7269\u3002\u8fd9\u6709\u52a9\u4e8e\u8bca\u65ad\u548c\u6cbb\u7597\u7b56\u7565\u7684\u5f00\u53d1\u3002<\/p>\n

2\u3001\u6570\u636e\u53ef\u89c6\u5316\uff1aKEGG\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u53ef\u4ee5\u901a\u8fc7\u751f\u6210\u56fe\u5f62\u5316\u5c55\u793a\u6765\u66f4\u597d\u5730\u5448\u73b0\u3002\u4f8b\u5982\uff0c\u4f7f\u7528\u67f1\u72b6\u56fe\u3001\u6563\u70b9\u56fe\u6216\u7f51\u7edc\u56fe\u7b49\u65b9\u5f0f\u5c06\u5bcc\u96c6\u901a\u8def\/\u529f\u80fd\u53ca\u5176\u5173\u8054\u57fa\u56e0\u53ef\u89c6\u5316\uff0c\u6709\u52a9\u4e8e\u76f4\u89c2\u5730\u7406\u89e3\u6574\u4f53\u7ed3\u6784\u548c\u76f8\u4e92\u4f5c\u7528\u3002<\/p>\n

3\u3001\u5047\u8bbe\u9a8c\u8bc1\u548c\u65b0\u5047\u8bbe\u751f\u6210\uff1a\u6839\u636e\u5df2\u77e5\u7684KEGG\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\uff0c\u53ef\u4ee5\u9a8c\u8bc1\u9884\u5148\u8bbe\u5b9a\u7684\u5047\u8bbe\u6216\u751f\u6210\u65b0\u7684\u751f\u7269\u5b66\u5047\u8bbe\u3002\u4f8b\u5982\uff0c\u5982\u679c\u67d0\u4e2a\u901a\u8def\u5728\u75be\u75c5\u4e2d\u663e\u8457\u5bcc\u96c6\uff0c\u5219\u53ef\u80fd\u63d0\u793a\u8be5\u901a\u8def\u5728\u75be\u75c5\u53d1\u5c55\u8fc7\u7a0b\u4e2d\u8d77\u91cd\u8981\u4f5c\u7528\u3002<\/p>\n

4\u3001\u6570\u636e\u6316\u6398\u548c\u6574\u5408\uff1a\u901a\u8fc7\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e0eKEGG\u6570\u636e\u5e93\u8fdb\u884c\u6574\u5408\u548c\u5206\u6790\uff0c\u53ef\u4ee5\u4ece\u5927\u89c4\u6a21\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\u63d0\u53d6\u6709\u5173\u7279\u5b9a\u901a\u8def\u3001\u529f\u80fd\u6216\u4ee3\u8c22\u9014\u5f84\u7684\u91cd\u8981\u4fe1\u606f\u3002\u8fd9\u6709\u52a9\u4e8e\u63ed\u793a\u6f5c\u5728\u7684\u8c03\u8282\u673a\u5236\u3001\u76f8\u4e92\u4f5c\u7528\u7f51\u7edc\u548c\u751f\u7269\u5b66\u8fc7\u7a0b\u3002<\/p>\n

\u603b\u4e4b\uff0cKEGG\u5bcc\u96c6\u5206\u6790\u662f\u4e00\u79cd\u5f3a\u5927\u800c\u5e7f\u6cdb\u5e94\u7528\u7684\u5de5\u5177\uff0c\u5728\u57fa\u56e0\u7ec4\u5b66\u3001\u8f6c\u5f55\u7ec4\u5b66\u548c\u4ee3\u8c22\u7ec4\u5b66\u7b49\u9886\u57df\u4e2d\u53d1\u6325\u7740\u91cd\u8981\u4f5c\u7528\u3002\u5b83\u5e2e\u52a9\u89e3\u91ca\u57fa\u56e0\u96c6\u5408\u5728\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u6240\u626e\u6f14\u7684\u89d2\u8272\uff0c\u5e76\u4e3a\u8fdb\u4e00\u6b65\u7814\u7a76\u63d0\u4f9b\u4e86\u65b9\u5411\u548c\u6d1e\u89c1\u3002<\/p>\n

\u5982\u679c\u9047\u5230\u4e0d\u61c2\u7684\u4e5f\u53ef\u4ee5\u501f\u52a9\u7ebf\u4e0a\u7684\u4e91\u5e73\u53f0\u54e6\uff5ehttp:\/\/www.biocloudservice.com\/home.html<\/p>\n

\u597d\u4e86\u4eca\u5929\u7684KEGG\u5bcc\u96c6\u5206\u6790\u5c31\u8bb2\u5230\u8fd9\u91cc\uff0c\u6b22\u8fce\u5927\u5bb6\u6709\u95ee\u9898\u4e0e\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u54e6\uff5e<\/p>\n","protected":false},"excerpt":{"rendered":"

\u539f\u7406\u7b80\u4ecb KEGG\u5bcc\u96c6\u5206\u6790\u662f\u4e00\u79cd\u751f\u7269\u4fe1\u606f\u5b66\u65b9\u6cd5\uff0c\u7528\u4e8e\u89e3\u91ca\u548c\u7406\u89e3\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u7684\u529f\u80fd\u548c\u53c2\u4e0e\u7684\u4ee3\u8c22\u901a\u8def\u3002\u8be5\u5206\u6790\u4f7f\u7528K […]<\/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\/25872"}],"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=25872"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25872\/revisions"}],"predecessor-version":[{"id":25880,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25872\/revisions\/25880"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25872"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25872"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25872"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}