{"id":29060,"date":"2024-02-20T17:52:32","date_gmt":"2024-02-20T09:52:32","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29060"},"modified":"2024-02-20T17:52:34","modified_gmt":"2024-02-20T09:52:34","slug":"%e5%88%a9%e7%94%a8%e6%a3%92%e6%a3%92%e7%b3%96%e5%9b%be%e5%b1%95%e7%a4%ba%e5%8d%95%e7%bb%86%e8%83%9emarker%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be%e9%87%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29060","title":{"rendered":"\u5229\u7528\u68d2\u68d2\u7cd6\u56fe\u5c55\u793a\u5355\u7ec6\u80demarker\u57fa\u56e0\u8868\u8fbe\u91cf"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u60f3\u7528\u68d2\u68d2\u7cd6\u56fe\u6765\u5c55\u793a\u5355\u7ec6\u80demarker\u57fa\u56e0\u5728\u4e0d\u540c\u7ec6\u80de\u7fa4\u91cc\u7684\u8868\u8fbe\u91cf\u60c5\u51b5\uff0c\u5c55\u793a\u51fa\u7684\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u5355\u7ec6\u80de\u6570\u636e\u6765\u81ea\u4ee5\u524d\u63a8\u6587\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u7ed3\u679c\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u7cfb\u7edf\u5b66\u4e60\u4e00\u4e0b\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u6d41\u7a0b\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

    install.packages(\u201cBiocManager\u201d)<\/p>\n

    BiocManager::install(\u201cSeurat\u201d)<\/p>\n

    install.packages(\u201cggsci\u201d)<\/p>\n

    install.packages(\u201creshape2\u201d)<\/p>\n

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

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

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

      library(Seurat)<\/p>\n

      library(ggsci)<\/p>\n

      library(reshape2)<\/p>\n

      library(tidyverse)<\/p>\n

      library(ggplot2)<\/p>\n

      3.\u5f00\u59cb\u7ed8\u56fe<\/p>\n

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

      gene <- c(“CD3E”,”MS4A1″,”GNLY”,”CD14″)<\/p>\n

      #\u8ba1\u7b97\u5e73\u5747\u8868\u8fbe\u91cf<\/p>\n

      Idents(pbmc) <- “seurat_clusters”<\/p>\n

      AveExpression <- AverageExpression(pbmc, assays = “RNA”, features = gene,verbose = TRUE) %>% .$RNA %>%as.data.frame<\/p>\n

      #\u5c06\u884c\u540d\u8f6c\u6362\u4e3a\u5217<\/p>\n

      AveExpression$Gene <- rownames(AveExpression)<\/p>\n

      #\u957f\u5bbd\u6570\u636e\u8f6c\u6362<\/p>\n

      df <- melt(AveExpression,id.vars= “Gene”)<\/p>\n

      colnames(df) <- c(“Gene”, “Cluster”, “Expression”)<\/p>\n

      #\u5bf9\u8868\u8fbe\u91cf\u8fdb\u884c\u8bbe\u7f6e<\/p>\n

      df$Expression[which(df$Expression>10)] <- 10 ####\u8bbe\u7f6e\u5e73\u5747\u8868\u8fbe\u91cf\u5927\u4e8e10\u7684\u503c\u4e3a10<\/p>\n

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

      p1 <- ggplot(df,aes(x=Gene, y=Expression))+<\/p>\n

      geom_hline(yintercept = seq(0, 10, 2.5),linetype = 2, color = “lightgray”,size=1)+<\/p>\n

      geom_segment(aes(x=Gene,xend=Gene,y=0,yend=Expression),color=”lightgray”,size = 1.5)+<\/p>\n

      geom_point(size=3,aes(color=Gene))+<\/p>\n

      scale_color_npg() +<\/p>\n

      theme_bw()+<\/p>\n

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

      labs(x=””,y=”Gene expression”)<\/p>\n

      #\u5206\u9762<\/p>\n

      p1 <- facet(p1, facet.by = “Cluster”,ncol = length(unique(df$Cluster)),panel.labs.font = list(size = 12),panel.labs.background = list(fill = “#a6cee3”))<\/p>\n

      #\u8c03\u6574\u4e3b\u9898<\/p>\n

      p1 <- p1 + scale_y_continuous(position = “right”)+ ####\u7528\u6765\u5c06y\u8f74\u79fb\u52a8\u4f4d\u7f6e<\/p>\n

      theme(axis.text.y = element_text(size=12, colour = “black”))+<\/p>\n

      theme(axis.text.x = element_blank())+ ## \u5220\u53bbX\u8f74\u6240\u6709\u523b\u5ea6\u6807\u7b7e<\/p>\n

      theme(axis.title.y = element_text(size=12, colour = “black”))+<\/p>\n

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

      theme(legend.position = “right”,<\/p>\n

      panel.border = element_blank(),## \u53bb\u6389\u6700\u5916\u5c42\u7684\u6b63\u65b9\u5f62\u8fb9\u6846<\/p>\n

      axis.ticks.x = element_line(color = NA))<\/p>\n

      \"Dingtalk_20230313092449\"<\/p>\n

      \u5c0f\u679c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u9700\u8981\u5728\u6027\u80fd\u597d\u7684\u670d\u52a1\u5668\u8fdb\u884c\u6570\u636e\u5206\u6790\uff0c\u5c0f\u679c\u5b89\u5229\u672c\u516c\u53f8\u670d\u52a1\u5668\uff0c\u5df2\u5b89\u88c5\u6240\u6709\u5355\u7ec6\u80de\u5206\u6790\u8f6f\u4ef6\u548cR\u5305\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\uff0c\u4e0b\u671f\u518d\u89c1\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

      \u4eca\u5929\u5c0f\u679c\u60f3\u7528\u68d2\u68d2\u7cd6\u56fe\u6765\u5c55\u793a\u5355\u7ec6\u80demarker\u57fa\u56e0\u5728\u4e0d\u540c\u7ec6\u80de\u7fa4\u91cc\u7684\u8868\u8fbe\u91cf\u60c5\u51b5\uff0c\u5c55\u793a\u51fa\u7684\u6548\u679c\u975e\u5e38\u4e0d\u9519\uff0c\u5355\u7ec6\u80de\u6570\u636e\u6765 […]<\/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\/29060"}],"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=29060"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29060\/revisions"}],"predecessor-version":[{"id":29062,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29060\/revisions\/29062"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29060"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29060"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29060"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}