{"id":29449,"date":"2024-02-22T18:06:15","date_gmt":"2024-02-22T10:06:15","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29449"},"modified":"2024-02-22T18:06:17","modified_gmt":"2024-02-22T10:06:17","slug":"%e8%b7%9f%e7%9d%80%e8%80%81%e4%bf%8a%e4%bf%8a%e5%a4%a7%e7%a5%9e%e5%ad%a6%e4%b9%a0clustergvis%e8%bf%9b%e8%a1%8c%e5%8d%95%e7%bb%86%e8%83%9e%e6%95%b0%e6%8d%ae%e5%8f%af%e8%a7%86%e5%8c%96","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29449","title":{"rendered":"\u8ddf\u7740\u8001\u4fca\u4fca\u5927\u795e\u5b66\u4e60ClusterGVis\u8fdb\u884c\u5355\u7ec6\u80de\u6570\u636e\u53ef\u89c6\u5316"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u60f3\u4e3a\u5927\u5bb6\u5b89\u5229\u4e00\u4e2aR\u5305ClusterGVis\uff0c\u8be5\u5305\u7531\u8001\u4fca\u4fca\u5f00\u53d1\uff0c\u524d\u671f\u8be5\u5305\u53ef\u4ee5\u8fdb\u884cBluk-seq\u8868\u8fbe\u77e9\u9635\u7684\u5904\u7406\uff0c\u53ef\u4ee5\u540c\u65f6\u7ed8\u5236\u805a\u7c7b+\u5206\u7ec4\u8868\u8fbe\u8d8b\u52bf\u6298\u7ebf\u56fe+\u529f\u80fd\u6ce8\u91ca\u7684\u7ec4\u5408\u56fe\uff0c\u901a\u8fc7\u4e00\u5f20\u70ed\u56fe\u53ef\u4ee5\u4e86\u89e3\u5dee\u5f02\u57fa\u56e0\u53ef\u4ee5\u5212\u5206\u6210\u51e0\u4e2acluster,\u6bcf\u4e2acluster\u7684\u8868\u8fbe\u968f\u7740\u65f6\u95f4\u662f\u5982\u4f55\u53d8\u5316\uff0c\u4ee5\u53ca\u8fd9\u4e9bcluster\u53d8\u5316\u7684\u57fa\u56e0\u901a\u8fc7GO\u6216\u8005KEGG\u529f\u80fd\u6ce8\u91ca\u4e86\u89e3\u5176\u529f\u80fd\uff1b\u6700\u8fd1\u770b\u5230\u8be5\u5305\u53ef\u4ee5\u5bf9\u63a5\u5355\u7ec6\u80de\u6570\u636e\u4e86\uff0c\u589e\u52a0\u4e86 prepareDataFromscRNA \u51fd\u6570\u6765\u6574\u7406\u51c6\u5907\u5355\u7ec6\u80de\u7684\u6570\u636e\uff0c\u53ef\u4ee5\u7ed8\u5236\u51fa\u50cfBluk-seq\u4e00\u6837\u7684\u7ec4\u5408\u56fe\uff0c\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u5c0f\u679c\u63a5\u4e0b\u6765\u5c31\u548c\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60\u8be5\u5305\u7684\u7528\u6cd5\uff0c\u5982\u4f55\u5bf9\u63a5\u5355\u7ec6\u80de\u6570\u636e\uff0c\u8bdd\u4e0d\u591a\u8bf4\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

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

    #\u91cd\u65b0\u5b89\u88c5\u83b7\u5f97\u6b64\u529f\u80fd\uff0c\u5982\u679c\u4ee5\u524d\u6ca1\u6709\u5b89\u88c5\u53ef\u4ee5\u5ffd\u7565\uff0c\u76f4\u63a5\u5b89\u88c5\u5c31\u53ef\u4ee5<\/p>\n

    install.packages(“devtools”)<\/p>\n

    devtools::install_github(“junjunlab\/ClusterGVis”)<\/p>\n

    BiocManager::install(\u201corg.Hs.eg.db\u201d)<\/p>\n

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

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

      library(ClusterGVis)<\/p>\n

      library(org.Hs.eg.db)<\/p>\n

      library(ggplot2)<\/p>\n

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

        #\u5bfc\u5165\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790\u7ed3\u679c\u6587\u4ef6<\/p>\n

        load(“pbmc.rda”)<\/p>\n

        #\u5355\u7ec6\u80de\u6570\u636e\u7ec6\u80de\u7fa4\u8fdb\u884c\u6ce8\u91ca<\/p>\n

        new.cluster.ids <- c(“Naive CD4 T”, “CD14+ Mono”, “Memory CD4 T”, “B”, “CD8 T”, “FCGR3A+ Mono”\uff0c”NK”, “DC”, “Platelet”)<\/p>\n

        names(new.cluster.ids) <- levels(pbmc)<\/p>\n

        pbmc <- RenameIdents(pbmc, new.cluster.ids)<\/p>\n

        #\u5bfb\u627emarker\u57fa\u56e0<\/p>\n

        pbmc.markers.all <- Seurat::FindAllMarkers(pbmc,<\/p>\n

        only.pos = TRUE,<\/p>\n

        min.pct = 0.25,<\/p>\n

        logfc.threshold = 0.25)<\/p>\n

        #\u6311\u9009\u8868\u8fbe\u91cf\u524d\u5341\u7684marker\u57fa\u56e0<\/p>\n

        pbmc.markers <- pbmc.markers.all %>%<\/p>\n

        dplyr::group_by(cluster) %>%<\/p>\n

        dplyr::top_n(n = 20, wt = avg_log2FC)<\/p>\n

        #\u5229\u7528prepareDataFromscRNA\u51fd\u6570\u51c6\u5907\u6570\u636e,showAverage \u53c2\u6570\u8bbe\u4e3a TRUE \u5219\u8868\u793a\u5bf9 \u57fa\u56e0\u7ec6\u80de\u4e9a\u7fa4\u4e00\u6837\u7684\u7ec6\u80de\u53d6\u5747\u503c\u8fdb\u884c\u7ed8\u56fe,\u5426\u5219\u5c31\u662f\u6240\u6709\u7ec6\u80de\u8fdb\u884c\u7ed8\u56fe,\u9ed8\u8ba4\u4f7f\u7528 seurat \u5bf9\u8c61\u7684 RNA assay \u7684 data \u6570\u636e\u3002<\/p>\n

        st.data <- prepareDataFromscRNA(object = pbmc,<\/p>\n

        diffData = pbmc.markers,<\/p>\n

        showAverage = TRUE)<\/p>\n

        #\u5bf9\u6bcf\u4e2acluster\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u8fd9\u91cc\u91c7\u7528GO\u5bcc\u96c6\u5206\u6790\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u9009\u62e9kegg\u5bcc\u96c6\u5206\u6790<\/p>\n

        enrich <- enrichCluster(object = st.data,<\/p>\n

        OrgDb = org.Hs.eg.db,<\/p>\n

        type = “BP”,<\/p>\n

        organism = “hsa”,<\/p>\n

        pvalueCutoff = 0.5,<\/p>\n

        topn = 5,<\/p>\n

        seed = 5201314)<\/p>\n

        #\u6311\u9009\u9700\u8981\u5c55\u793a\u7684marker\u57fa\u56e0<\/p>\n

        markGenes = unique(pbmc.markers$gene)[sample(1:length(unique(pbmc.markers$gene)),40,<\/p>\n

        replace = F)]<\/p>\n

        #\u7ed8\u5236cluster\u57fa\u56e0\u8868\u8fbe\u6298\u7ebf\u56fe<\/p>\n

        visCluster(object = st.data,<\/p>\n

        plot.type = “line”)<\/p>\n

        \"Dingtalk_20230316134356\"<\/p>\n

        #\u7ed8\u5236\u70ed\u56fe<\/p>\n

        pdf(‘sc1.pdf’,height = 10,width = 6,onefile = F)<\/p>\n

        visCluster(object = st.data,<\/p>\n

        plot.type = “heatmap”,<\/p>\n

        column_names_rot = 45,<\/p>\n

        markGenes = markGenes,<\/p>\n

        cluster.order = c(1:9))<\/p>\n

        dev.off()<\/p>\n

        \"Dingtalk_20230316134610\"<\/p>\n

        #\u7ed8\u5236\u70ed\u56fe\u5e76\u6dfb\u52a0\u5bcc\u96c6\u6ce8\u91ca\u548c\u5206\u7ec4\u6298\u7ebf\u56fe<\/p>\n

        pdf(‘sc2.pdf’,height = 10,width = 14,onefile = F)<\/p>\n

        visCluster(object = st.data,<\/p>\n

        plot.type = “both”,<\/p>\n

        column_names_rot = 45,<\/p>\n

        show_row_dend = F,<\/p>\n

        markGenes = markGenes,<\/p>\n

        markGenes.side = “left”,<\/p>\n

        annoTerm.data = enrich,<\/p>\n

        line.side = “left”,<\/p>\n

        cluster.order = c(1:9),<\/p>\n

        go.col = rep(jjAnno::useMyCol(“stallion”,n = 9),each = 5),<\/p>\n

        add.bar = T)<\/p>\n

        dev.off()<\/p>\n

        \"Dingtalk_20230316135010\"<\/p>\n

        \u5c0f\u679c\u4eca\u5929\u5bf9ClusterGVis\u5305\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u8be5\u5305\u5bf9\u4e8e\u8f6c\u5f55\u7ec4\u6570\u636e\u7684\u53ef\u89c6\u5316\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u53ef\u4ee5\u7528\u4e00\u5f20\u70ed\u56fe\u6765\u5c55\u793a\u57fa\u56e0\u7684\u8868\u8fbe\u6a21\u5f0f\uff0c\u805a\u7c7b\u548c\u529f\u80fd\u6ce8\u91ca\uff0c\u529f\u80fd\u6ce8\u91ca\u5305\u62ec\u4e86\u5e38\u89c1\u7684GO\u548cKEGG,\u7528\u8d77\u6765\u8d85\u7ea7\u65b9\u4fbf\uff0c\u503c\u5f97\u63a8\u8350\uff0c\u611f\u5174\u8da3\u7684\u53ef\u4ee5\u53bbgithub(https:\/\/github.com\/junjunlab\/ClusterGVis)\u6df1\u5165\u5b66\u4e60\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u5965\uff0c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u4e86,\u89c9\u5f97\u4e0d\u9519\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u70b9\u8d5e\u52a0\u5173\u6ce8\u5965\uff0c\u4e0b\u671f\u518d\u89c1\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5c0f\u679c\u60f3\u4e3a\u5927\u5bb6\u5b89\u5229\u4e00\u4e2aR\u5305ClusterGVis\uff0c\u8be5\u5305\u7531\u8001\u4fca\u4fca\u5f00\u53d1\uff0c\u524d\u671f\u8be5\u5305\u53ef\u4ee5\u8fdb\u884cBluk-seq\u8868\u8fbe\u77e9\u9635 […]<\/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\/29449"}],"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=29449"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29449\/revisions"}],"predecessor-version":[{"id":29453,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29449\/revisions\/29453"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29449"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29449"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29449"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}