{"id":29056,"date":"2024-02-20T17:49:03","date_gmt":"2024-02-20T09:49:03","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29056"},"modified":"2024-02-20T17:49:04","modified_gmt":"2024-02-20T09:49:04","slug":"%e5%88%a9%e7%94%a8ggplot2%e7%bb%98%e5%88%b6%e6%9b%bc%e5%93%88%e9%a1%bf%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29056","title":{"rendered":"\u5229\u7528ggplot2\u7ed8\u5236\u66fc\u54c8\u987f\u56fe"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u60f3\u901a\u8fc7ggplot2\u6765\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\uff0c\u5229\u7528\u66fc\u54c8\u987f\u56fe\u5c55\u793a\u5fae\u751f\u7269\u7269\u79cd\u4e30\u5ea6\u5dee\u5f02\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u9700\u8981\u7684R \u5305<\/li>\n<\/ol>\n

    install.packages(\u201cggplot2\u201d)<\/p>\n

    install.packages(\u201ctidyverse\u201d)<\/p>\n

    install.packages(\u201cggrepel\u201d)<\/p>\n

      \n
    1. \u8f7d\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(ggplot2)<\/p>\n

      library(tidyverse)<\/p>\n

      library(ggrepel)<\/p>\n

        \n
      1. \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n

        #\u8bfb\u5165\u6570\u636e<\/p>\n

        df<-read.table(\u201cOTU.txt\u201d, header=T, row.names=1, sep=\u201d\\t\u201d, comment.char=\u201d\u201d)<\/p>\n

        \"Dingtalk_20230220143853\"<\/p>\n

        #\u8ba1\u7b97 x \u8f74\u6807\u7b7e\u3001\u77e9\u5f62\u533a\u5757\u5bf9\u5e94\u7684 x \u8f74\u4f4d\u7f6e<\/p>\n

        getBreak<-function(x,y){<\/p>\n

        freq<-as.vector(table(y))<\/p>\n

        half_freq<-freq%\/%2<\/p>\n

        for (i in seq(2,length(freq))){<\/p>\n

        new_num<-freq[i]+freq[i-1]<\/p>\n

        freq[i]=new_num}<\/p>\n

        pos<-freq-half_freq<\/p>\n

        break_point<-as.vector(x[pos])<\/p>\n

        return(break_point)<\/p>\n

        }<\/p>\n

        #\u8bbe\u7f6e\u5206\u7ec4\u989c\u8272<\/p>\n

        cols<-c(“#008087″,”#00A962″,”#86C03D”,”#74BC56″,<\/p>\n

        “#E53636″,”#3D7ABB”,”#EE8B15″,”#AF4592″,<\/p>\n

        “#7AC5C1″,”#906024″,”#6E1F86″,”#545556″)<\/p>\n

        #\u8bbe\u7f6e\u9608\u503c\u7ebf<\/p>\n

        threshold<–log10(0.05)<\/p>\n

        #\u7b5b\u9009\u8d85\u8fc7\u9608\u503c\u7ebf\u7684\u70b9<\/p>\n

        gtext<-filter(df,df$P< 0.05)<\/p>\n

        #\u5f00\u59cb\u7ed8\u56fe<\/p>\n

        p<-ggplot(df, aes(x=OTU, y=NegativeLogP, color=Group, size=RA, shape=Level)) +<\/p>\n

        geom_point(alpha=.7,key_glyph=”point”)+<\/p>\n

        scale_shape_manual(values=c(16,1))+ #\u9009\u62e9\u5f62\u72b6\uff0cnosig\u5bf9\u5e94\u7a7a\u5fc3\u5706\uff0cenrich\u5bf9\u5e94\u5b9e\u5fc3\u5706<\/p>\n

        scale_size_continuous(range = c(0.5,5),<\/p>\n

        breaks = c(0.05, 0.10,0.50,1.00,5.00),<\/p>\n

        labels = c(‘0.05’, ‘0.10’,’0.50′,’1.00′,’5.00′))+ #\u8bbe\u7f6e\u6563\u70b9\u5c3a\u5bf8<\/p>\n

        guides(color=”none”,shape=”none”)+#\u9690\u85cf\u56fe\u4f8b<\/p>\n

        scale_x_discrete(breaks=getBreak(df$OTU,df$Group), labels=c(“Alphaproteobacteria”,”Betaproteobacteria”,”Gammaproteobacteria”,”Deltaproteobacteria”,”Acidobacteria”,”Actinobacteria”,”Bacteroidetes”,”Chloroflexi”,”Gemdfimonadetes”,”Firmicutes”,”Planctomycetes”,”Others”),<\/p>\n

        expand = expansion(mult = 0.03))+<\/p>\n

        geom_text_repel(aes(OTU,NegativeLogP,label=OTU),gtext,colour=’black’, size =5,box.padding = 1,<\/p>\n

        point.padding = 0.8,<\/p>\n

        segment.color = “black”,<\/p>\n

        show.legend = F)+#\u6dfb\u52a0\u6587\u5b57\u6807\u7b7e<\/p>\n

        geom_hline(yintercept=threshold, linetype=”dashed”, color=”red”)+<\/p>\n

        labs(x=””, y=”-log10(P)”)+<\/p>\n

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

        theme(axis.line = element_line(size = 1),<\/p>\n

        panel.grid=element_blank(),<\/p>\n

        panel.background = element_rect(fill = ‘white’),<\/p>\n

        axis.text.x = element_text(angle = 45, hjust = 0.5, vjust = 0.5))<\/p>\n

        #\u4fdd\u5b58\u56fe\u7247<\/p>\n

        ggsave(“manhan.pdf”, p, height = 5,width = 10)<\/p>\n

        \"Dingtalk_20230220143738\"<\/p>\n

        \u6700\u7ec8\u7ed8\u5236\u51fa\u4e86\u60f3\u8981\u7684\u66fc\u54c8\u987f\u56fe\uff0c\u6548\u679c\u770b\u8d77\u6765\u8fd8\u4e0d\u9519\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\uff0c\u5c0f\u679c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u60f3\u901a\u8fc7ggplot2\u6765\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\uff0c\u5229\u7528\u66fc\u54c8\u987f\u56fe\u5c55\u793a\u5fae\u751f\u7269\u7269\u79cd\u4e30\u5ea6\u5dee\u5f02\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u9700\u8981\u7684R \u5305 […]<\/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\/29056"}],"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=29056"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29056\/revisions"}],"predecessor-version":[{"id":29059,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29056\/revisions\/29059"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29056"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29056"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29056"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}