{"id":29199,"date":"2024-02-21T17:34:45","date_gmt":"2024-02-21T09:34:45","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29199"},"modified":"2024-02-21T17:34:46","modified_gmt":"2024-02-21T09:34:46","slug":"%e5%88%a9%e7%94%a8ggclusternet%e7%bb%98%e5%88%b6%e5%85%b1%e7%ba%bf%e7%bd%91%e7%bb%9c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29199","title":{"rendered":"\u5229\u7528ggClusterNet\u7ed8\u5236\u5171\u7ebf\u7f51\u7edc"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u5b66\u4e60\u4e00\u4e0bggClusterNet\u8fd9\u4e2a\u5305\uff0c\u8fdb\u884c\u5171\u7ebf\u7f51\u7edc\u7684\u7ed8\u5236\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

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

    install.packages(\u201cigraph\u201d)<\/p>\n

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

    install.packages(\u201cphyloseq\u201d)<\/p>\n

    install.packages(\u201csna\u201d)<\/p>\n

    install.packages(\u201cdevtools\u201d)<\/p>\n

    install.packages(\u201ctidyfst\u201d)<\/p>\n

    devtools::install_github(“taowenmicro\/ggClusterNet”)<\/p>\n

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

      \n
    1. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(igraph)<\/p>\n

      library(phyloseq)<\/p>\n

      library(sna)<\/p>\n

      library(ggClusterNet)<\/p>\n

      library(ggplot2)<\/p>\n

      library(tidyfst)<\/p>\n

      library(tidyverse)<\/p>\n

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

        #\u5bfc\u5165\u793a\u4f8b\u6570\u636e#<\/p>\n

        data(ps)<\/p>\n

        #-\u63d0\u53d6\u4e30\u5ea6\u6700\u9ad8\u7684\u6307\u5b9a\u6570\u91cf\u7684otu\u8fdb\u884c\u6784\u5efa\u7f51\u7edc<\/p>\n

        #\u8ba1\u7b97\u76f8\u5173#<\/p>\n

        result = corMicro (ps = ps,<\/p>\n

        N = 150,<\/p>\n

        method.scale = “TMM”,<\/p>\n

        r.threshold=0.8,<\/p>\n

        p.threshold=0.05,<\/p>\n

        method = “spearman”<\/p>\n

        )<\/p>\n

        #\u63d0\u53d6\u76f8\u5173\u77e9\u9635<\/p>\n

        cor = result[[1]]<\/p>\n

        head(cor)<\/p>\n

        #\u7f51\u7edc\u4e2d\u5305\u542b\u7684OTU\u7684phyloseq\u6587\u4ef6\u63d0\u53d6<\/p>\n

        ps_net = result[[3]]<\/p>\n

        #-\u5bfc\u51faotu\u8868\u683c<\/p>\n

        otu_table = ps_net %>%<\/p>\n

        vegan_otu() %>%<\/p>\n

        t() %>%<\/p>\n

        as.data.frame()<\/p>\n

        #\u4eba\u5de5\u6784\u9020\u5206\u7ec4\u4fe1\u606f\uff1a\u5c06\u7f51\u7edc\u4e2d\u5168\u90e8OTU\u5206\u4e3a\u4e94\u4e2a\u90e8\u5206<\/p>\n

        netClu=data.frame(ID=row.names(otu_table),group=rep(1:5,length(row.names(otu_table)))[1:length(row.names(otu_table))] )<\/p>\n

        netClu$group = as.factor(netClu$group)<\/p>\n

        #\u8ba1\u7b97\u5e03\u5c40#<\/p>\n

        result2 = PolygonClusterG (cor = cor,nodeGroup =netClu )<\/p>\n

        node = result2[[1]]<\/p>\n

        #nodeadd \u8282\u70b9\u6ce8\u91ca\u7684\uff1a\u7528otu\u8868\u683c\u548c\u5206\u7ec4\u6587\u4ef6\u8fdb\u884c\u6ce8\u91ca<\/p>\n

        #nodeadd\u51fd\u6570\u53ea\u662f\u63d0\u4f9b\u4e86\u7b80\u5355\u7684\u7528\u6ce8\u91ca\u51fd\u6570\uff0c\u7528\u6237\u53ef\u4ee5\u81ea\u5df1\u5728node\u7684\u8868\u683c\u540e\u9762\u6dfb\u52a0\u5404\u79cd\u6ce8\u91ca\u4fe1\u606f<\/p>\n

        tax_table = ps_net %>%<\/p>\n

        vegan_tax() %>%<\/p>\n

        as.data.frame()<\/p>\n

        #node\u8282\u70b9\u6ce8\u91ca#<\/p>\n

        nodes = nodeadd(plotcord =node,otu_table = otu_table,tax_table = tax_table)<\/p>\n

        #\u8ba1\u7b97\u8fb9#<\/p>\n

        edge = edgeBuild(cor = cor,node = node)<\/p>\n

        p <- ggplot() + geom_segment(aes(x = X1, y = Y1, xend = X2, yend = Y2,color = as.factor(cor)),<\/p>\n

        data = edge, size = 0.5) +<\/p>\n

        geom_point(aes(X1, X2,fill = Phylum,size = mean),pch = 21, data = nodes) +<\/p>\n

        scale_colour_brewer(palette = “Set1”) +<\/p>\n

        scale_x_continuous(breaks = NULL) + scale_y_continuous(breaks = NULL) +<\/p>\n

        theme(panel.background = element_blank()) +<\/p>\n

        theme(axis.title.x = element_blank(), axis.title.y = element_blank()) +<\/p>\n

        theme(legend.background = element_rect(colour = NA)) +<\/p>\n

        theme(panel.background = element_rect(fill = “white”, colour = NA)) +<\/p>\n

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

        ggsave(p,\u201cggcluster1.pdf\u201d)<\/p>\n

        \"Dingtalk_20230220160119\"<\/p>\n

        #\u52068\u7ec4<\/p>\n

        netClu=data.frame(ID=row.names(cor),group=rep(1:8,length(row.names(cor)))[1:length(row.names(cor))] )<\/p>\n

        netClu$group = as.factor(netClu$group)<\/p>\n

        result2 = PolygonClusterG (cor = cor,nodeGroup =netClu )<\/p>\n

        node = result2[[1]]<\/p>\n

        # node\u8282\u70b9\u6ce8\u91ca#<\/p>\n

        nodes = nodeadd(plotcord =node,otu_table = otu_table,tax_table = tax_table)<\/p>\n

        #\u8ba1\u7b97\u8fb9#<\/p>\n

        edge = edgeBuild(cor = cor,node = node)<\/p>\n

        ### \u51fa\u56fe<\/p>\n

        p1 <- ggplot() + geom_segment(aes(x = X1, y = Y1, xend = X2, yend = Y2,color = as.factor(cor)),<\/p>\n

        data = edge, size = 0.5) +<\/p>\n

        geom_point(aes(X1, X2,fill = Phylum,size = mean),pch = 21, data = nodes) +<\/p>\n

        scale_colour_brewer(palette = “Set1″) +<\/p>\n

        scale_x_continuous(breaks = NULL) + scale_y_continuous(breaks = NULL) +<\/p>\n

        # labs( title = paste(layout,”network”,sep = “_”))+<\/p>\n

        # geom_text_repel(aes(X1, X2,label=Phylum),size=4, data = plotcord)+<\/p>\n

        # discard default grid + titles in ggplot2<\/p>\n

        theme(panel.background = element_blank()) +<\/p>\n

        # theme(legend.position = “none”) +<\/p>\n

        theme(axis.title.x = element_blank(), axis.title.y = element_blank()) +<\/p>\n

        theme(legend.background = element_rect(colour = NA)) +<\/p>\n

        theme(panel.background = element_rect(fill = “white”, colour = NA)) +<\/p>\n

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

        ggsave(\u201cggCluster.2.pdf\u201d,p1)<\/p>\n

        \"Dingtalk_20230220160555\"<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u5b66\u4e60\u4e00\u4e0bggClusterNet\u8fd9\u4e2a\u5305\uff0c\u8fdb\u884c\u5171\u7ebf\u7f51\u7edc\u7684\u7ed8\u5236\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u9700\u8981\u7684R\u5305 install […]<\/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\/29199"}],"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=29199"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29199\/revisions"}],"predecessor-version":[{"id":29202,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29199\/revisions\/29202"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29199"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29199"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29199"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}