{"id":28888,"date":"2024-02-19T18:00:58","date_gmt":"2024-02-19T10:00:58","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28888"},"modified":"2024-02-19T18:01:00","modified_gmt":"2024-02-19T10:01:00","slug":"%e7%bb%98%e5%88%b6%e5%9f%ba%e5%9b%a0%e4%bd%8d%e7%bd%ae%e7%8e%af%e5%bd%a2%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28888","title":{"rendered":"\u7ed8\u5236\u57fa\u56e0\u4f4d\u7f6e\u73af\u5f62\u56fe"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u7ed8\u5236\u4e00\u4e0b\u57fa\u56e0\u4f4d\u7f6e\u7684\u73af\u5f62\u56fe\uff0c\u7ed8\u56fe\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u6240\u9700\u8981\u7684\u5305<\/li>\n<\/ol>\n

    BiocManager::install(\u201cRCircos\u201d)<\/p>\n

    install.packages(\u201cmagritter\u201d)<\/p>\n

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

    2\u5bfc\u5165\u9700\u8981\u7684R\u5305<\/p>\n

    library(RCircos)<\/p>\n

    library(magritter)<\/p>\n

    library(tidyverse)<\/p>\n

      \n
    1. \u8bfb\u53d6\u6570\u636e<\/li>\n<\/ol>\n

      #\u56fe\u4e2d\u5c55\u793a\u76ee\u6807\u57fa\u56e0\u6587\u4ef6<\/p>\n

      genes <- read.table(“gene.txt”, header = T)$SYMBOL<\/p>\n

      \"Dingtalk_20230131131824\"<\/p>\n

      # \u6839\u636e\u57fa\u56e0\u96c6\u63d0\u53d6\u51fa\u76ee\u7684\u57fa\u56e0\u6240\u5728\u4f4d\u7f6e<\/p>\n

      gene_pos <- import(“hg38.gtf”) %>% # \u8f7d\u5165gtf\u6587\u4ef6<\/p>\n

      as.data.frame %>%<\/p>\n

      # \u4ec5\u9009\u62e9\u57fa\u56e0\uff0c\u53bb\u9664\u8f6c\u5f55\u672c\u7b49\u7b49<\/p>\n

      filter(source == “HAVANA”, type == “gene”) %>%<\/p>\n

      # \u4fdd\u7559\u57fa\u56e0\u4f4d\u7f6e\u548c\u540d\u79f0<\/p>\n

      dplyr::select(seqnames, start, end, gene_name) %>%<\/p>\n

      # \u6311\u9009\u76ee\u7684\u57fa\u56e0<\/p>\n

      filter(gene_name %in% genes)<\/p>\n

      \"Dingtalk_20230131131959\"<\/p>\n

      # \u539f\u6587\u6ca1\u8bf4\u5185\u5708\u6563\u70b9\u56fe\u4ee3\u8868\u4ec0\u4e48\u7279\u5f81\uff0c\u6211\u4eec\u8fd9\u91cc\u968f\u673a\u751f\u6210\u4e00\u5217\u6570\u503c<\/p>\n

      gene_pos$gene_dot <- rnorm(nrow(gene_pos), 0, 2)<\/p>\n

      # \u4fdd\u5b58\u5230\u6587\u4ef6\uff0c\u4fbf\u4e8e\u5957\u7528\u683c\u5f0f<\/p>\n

      write.csv(gene_pos,”gene_pos.csv”, row.names = F, quote = F)<\/p>\n

      #\u52a0\u8f7d\u57fa\u56e0\u6240\u5728\u7684\u4f4d\u7f6e\u548c\u6570\u503c<\/p>\n

      gene_pos <- read.csv(“gene_pos.csv”, header = T)<\/p>\n

      # \u52a0\u8f7d\u67d3\u8272\u4f53Ideogram<\/p>\n

      (data(“UCSC.HG38.Human.CytoBandIdeogram”))<\/p>\n

      pdf(file=”circGene.pdf”, height=5, width=5)<\/p>\n

      # \u6839\u636ehg38\u6784\u5efa\u67d3\u8272\u4f53\u4f4d\u7f6e\uff0c\u53ea\u4fdd\u7559chr1-22,X,Y\uff0c\u5728\u5708\u5185\u90e8\u6784\u5efa\u4e09\u5708\u8f68\u9053<\/p>\n

      RCircos.Set.Core.Components(UCSC.HG38.Human.CytoBandIdeogram,<\/p>\n

      chr.exclude = NULL,<\/p>\n

      tracks.inside = 3,<\/p>\n

      tracks.outside = 0)<\/p>\n

      RCircos.Set.Plot.Area()<\/p>\n

      # \u7ed8\u5236\u67d3\u8272\u4f53<\/p>\n

      RCircos.Chromosome.Ideogram.Plot()<\/p>\n

      # \u5728\u7b2c\u4e00\u5708\u7528\u6563\u70b9\u5728\u57fa\u56e0\u6240\u5728\u7684\u4f4d\u7f6e\u6807\u6ce8\u6570\u503c<\/p>\n

      # \u8c03\u6574\u914d\u8272<\/p>\n

      params <- RCircos.Get.Plot.Parameters()<\/p>\n

      params$track.background <- “grey” # \u7b2c\u4e09\u5708\u9ed8\u8ba4\u914d\u8272\u4e3awheat\uff0c\u6a21\u4eff\u539f\u6587\u4fee\u6539\u4e3a\u7070\u8272<\/p>\n

      RCircos.Reset.Plot.Parameters(params)<\/p>\n

      RCircos.Scatter.Plot(gene_pos,<\/p>\n

      data.col = 5, # \u7528\u7b2c5\u5217\u7684\u6570\u503c\u4f5c\u4e3a\u70b9\u7684\u7eb5\u5750\u6807<\/p>\n

      by.fold = 1, # \u70b9\u7684\u989c\u8272cutoff\uff0c\u5927\u4e8e\u7b49\u4e8e1\u7684\u57fa\u56e0\u663e\u793a\u4e3a\u7ea2\u8272\u70b9\uff0c\u5c0f\u4e8e\u7b49\u4e8e-1\u7684\u663e\u793a\u4e3a\u84dd\u8272\u70b9\uff0c-1\u52301\u4e4b\u95f4\u4e3a\u9ed1\u70b9<\/p>\n

      track.num = 1,<\/p>\n

      side = “in”)<\/p>\n

      # \u5728\u7b2c\u4e8c\u5708\u7ed8\u5236\u7ebf\u6bb5\u6807\u6ce8\u57fa\u56e0\u6240\u5728\u7684\u4f4d\u7f6e<\/p>\n

      RCircos.Gene.Connector.Plot(genomic.data = gene_pos,<\/p>\n

      track.num = 2,<\/p>\n

      side = “in”)<\/p>\n

      # \u5728\u7b2c\u4e09\u5708\u6807\u6ce8\u57fa\u56e0\u540d<\/p>\n

      RCircos.Gene.Name.Plot(gene_pos,<\/p>\n

      name.col = 4,<\/p>\n

      track.num = 3,<\/p>\n

      side = “in”)<\/p>\n

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

      \"Dingtalk_20230131142420\"<\/p>\n

      \u5c0f\u679c\u6700\u7ec8\u7ed8\u5236\u51fa\u4e86\u76ee\u6807\u57fa\u56e0\u4f4d\u7f6e\u73af\u5f62\u56fe\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

      \u4eca\u5929\u5c0f\u679c\u7ed8\u5236\u4e00\u4e0b\u57fa\u56e0\u4f4d\u7f6e\u7684\u73af\u5f62\u56fe\uff0c\u7ed8\u56fe\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u6240\u9700\u8981\u7684\u5305 BiocManager::install(\u201c […]<\/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\/28888"}],"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=28888"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28888\/revisions"}],"predecessor-version":[{"id":28892,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28888\/revisions\/28892"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28888"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=28888"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=28888"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}