install.packages(\u201cBiocManager\u201d)<\/p>\n
BiocManager::install(“EnhancedVolcano”)<\/p>\n
install.packages(\u201ctidyverse\u201d)<\/p>\n
- \n
- \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n
library(BiocManager)<\/p>\n
library(tidyverse)<\/p>\n
library(EnhancedVolcano)<\/p>\n
- \n
- \u793a\u4f8b\u6570\u636e<\/li>\n<\/ol>\n
#\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6<\/p>\n
df <- read.table(“limma.txt”, header = T)<\/p>\n
![\"Dingtalk_20230306150513\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230306150513.jpeg?resize=640%2C209\")
<\/p>\n#\u76ee\u6807\u57fa\u56e0\u6587\u4ef6<\/p>\n
markergene<-read.table(“genelist”,header=T)$gene<\/p>\n
![\"Dingtalk_20230306150709\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230306150709.jpeg?resize=519%2C131\")
<\/p>\n- \n
- \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n
group<-ifelse(<\/p>\n
df$log2FC<(-1.5)&df$Pvalue<0.05,’#4D4398′,<\/p>\n
ifelse(df$log2FC>(1.5)&df$Pvalue<0.05,’#F18D00′,<\/p>\n
‘#b5b5b5’))<\/p>\n
group[is.na(group)]<-‘#b5b5b5′<\/p>\n
names(group)[group==’#F18D00’]<-‘Up’<\/p>\n
names(group)[group==’#b5b5b5′]<-‘Nosignif’<\/p>\n
names(group)[group==’#4D4398′]<-‘Down’<\/p>\n
#\u5f00\u59cb\u7ed8\u56fe<\/p>\n
EnhancedVolcano(df,<\/p>\n
x=”log2FC”,<\/p>\n
y=”Pvalue”,<\/p>\n
lab=df$gene,<\/p>\n
pCutoff=10e-1\/20,#y\u8f74\u9608\u503c\u7ebf(\u6c34\u5e73)<\/p>\n
FCcutoff=1.5,#x\u8f74\u9608\u503c\u7ebf\uff08\u5782\u76f4\uff09<\/p>\n
pointSize=3,#\u6563\u70b9\u5927\u5c0f<\/p>\n
labSize=3.5,#\u6807\u7b7e\u5927\u5c0f<\/p>\n
xlim=c(-6, 6),#X\u8f74\u8303\u56f4<\/p>\n
ylim=c(0,8),#Y\u8f74\u8303\u56f4<\/p>\n
selectLab=c(markergene),#\u4f7f\u7528selectLab\u53c2\u6570\u9009\u5b9a\u6240\u5173\u6ce8\u7684\u6807\u7b7e<\/p>\n
xlab=bquote(~Log[2]~’fold change’),#\u5c06\u5185\u5bb9\u4f20\u9012\u7ed9xlab<\/p>\n
labCol=’black’,#\u6807\u7b7e\u989c\u8272<\/p>\n
labFace=’bold’,#\u6807\u7b7e\u5b57\u4f53<\/p>\n
boxedLabels=TRUE,#\u662f\u5426\u5728\u6846\u4e2d\u7ed8\u5236\u6807\u7b7e<\/p>\n
drawConnectors=TRUE,#\u662f\u5426\u901a\u8fc7\u8fde\u7ebf\u5c06\u6807\u7b7e\u8fde\u63a5\u5230\u5bf9\u5e94\u7684\u70b9\u4e0a<\/p>\n
widthConnectors=0.8,#\u8fde\u7ebf\u7684\u5bbd\u5ea6<\/p>\n
endsConnectors=”last”,#\u8fde\u7ebf\u7ed8\u5236\u7bad\u5934\u7684\u65b9\u5411\uff0c\u53ef\u9009first\u3001both\u3001last<\/p>\n
colConnectors=’black’,#\u8fde\u7ebf\u7684\u989c\u8272<\/p>\n
colCustom=group,#\u7528group\u8986\u76d6\u9ed8\u8ba4\u914d\u8272\u65b9\u6848<\/p>\n
colAlpha=0.6,#\u8c03\u6574\u900f\u660e\u5ea6<\/p>\n
cutoffLineType=’dotdash’,#\u9608\u503c\u7ebf\u7c7b\u578b<\/p>\n
cutoffLineCol=’pink’,#\u9608\u503c\u7ebf\u989c\u8272<\/p>\n
cutoffLineWidth=0.88,#\u9608\u503c\u7ebf\u7c97\u7ec6<\/p>\n
title=”Volcano plot”,#\u4e3b\u6807\u9898<\/p>\n
subtitle=”Differential expression”,#\u526f\u6807\u9898<\/p>\n
caption=bquote(~Log[2]~”fold change cutoff,1;p-value cutoff,0.05″),#\u6ce8\u91ca\u8bf4\u660e<\/p>\n
legendPosition=’right’,#\u56fe\u4f8b\u4f4d\u7f6e<\/p>\n
legendLabSize=12,#\u56fe\u4f8b\u6587\u5b57\u5927\u5c0f<\/p>\n
legendIconSize=6)<\/p>\n
![\"Dingtalk_20230306153300\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230306153300.jpeg?resize=610%2C553\")
<\/p>\n\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\uff0c\u4e0b\u671f\u518d\u89c1\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
\u4eca\u5929\u5c0f\u679c\u53d1\u73b0\u4e00\u6b3e\u975e\u5e38\u4e0d\u9519\u7684R\u5305EnhancedVolcano\uff0c\u8be5\u5305\u753b\u51fa\u6765\u7684\u706b\u5c71\u56fe\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u706b\u5c71\u56fe\u7684\u989c\u503c\u975e\u5e38 […]<\/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\/29217"}],"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=29217"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29217\/revisions"}],"predecessor-version":[{"id":29221,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29217\/revisions\/29221"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29217"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29217"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29217"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
- \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n
- \u793a\u4f8b\u6570\u636e<\/li>\n<\/ol>\n