{"id":23705,"date":"2024-01-08T17:33:01","date_gmt":"2024-01-08T09:33:01","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23705"},"modified":"2024-01-08T17:33:03","modified_gmt":"2024-01-08T09:33:03","slug":"%e8%80%81%e5%8f%b8%e6%9c%ba%e5%b8%a6%e4%bd%a0%e4%b8%89%e5%88%86%e9%92%9f%e7%94%a8ggplot%e7%94%bb%e5%87%ba%e7%be%8e%e8%a7%82%e7%9a%84%e7%81%ab%e5%b1%b1%e5%9b%be%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23705","title":{"rendered":"\u8001\u53f8\u673a\u5e26\u4f60\u4e09\u5206\u949f\u7528ggplot\u753b\u51fa\u7f8e\u89c2\u7684\u706b\u5c71\u56fe\uff01"},"content":{"rendered":"

\u706b\u5c71\u56fe\u76f8\u4fe1\u5927\u5bb6\u80af\u5b9a\u90fd\u4e0d\u964c\u751f\uff0c\u4f46\u662f\u600e\u4e48\u753b\u51fa\u7f8e\u89c2\u800c\u53c8\u5927\u65b9\u7684\u706b\u5c71\u56fe\u53ef\u8ba9\u5f88\u591a\u5c0f\u4f19\u4f34\u6293\u8033\u6320\u816e\u4e86\uff0c\u4e0b\u9762\u5c0f\u679c\u5316\u8eab\u8001\u53f8\u673a\u5e26\u5c0f\u4f19\u4f34\u4eec\u4e00\u540c\u5b66\u4e60\u753b\u76f4\u89c2\u7684\u706b\u5c71\u56fe\u5427<\/p>\n

\u706b\u5c71\u56fe\u662f\u6563\u70b9\u56fe\u7684\u4e00\u79cd\uff0c\u5b83\u5c06\u7edf\u8ba1\u6d4b\u8bd5\u4e2d\u7684\u7edf\u8ba1\u663e\u8457\u6027\u91cf\u5ea6\uff08\u5982p value\uff09\u548c\u53d8\u5316\u5e45\u5ea6\u76f8\u7ed3\u5408\uff0c\u4ece\u800c\u80fd\u591f\u5e2e\u52a9\u5feb\u901f\u76f4\u89c2\u5730\u8bc6\u522b\u90a3\u4e9b\u53d8\u5316\u5e45\u5ea6\u8f83\u5927\u4e14\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u7684\u6570\u636e\u70b9\uff08\u57fa\u56e0\u7b49\uff09\u3002<\/p>\n

\u706b\u5c71\u56fe\u5e38\u5e94\u7528\u4e8e\u8f6c\u5f55\u7ec4\u7814\u7a76\uff0c\u4e5f\u80fd\u5e94\u7528\u4e8e\u57fa\u56e0\u7ec4\uff0c\u86cb\u767d\u8d28\u7ec4\uff0c\u4ee3\u8c22\u7ec4\u7b49\u7edf\u8ba1\u6570\u636e\u3002\u706b\u5c71\u56fe\u7684\u6a2a\u8f74\u4e00\u822c\u662f Log2 (fold change) \uff0c\u8868\u793a\u4e24\u7ec4\u6837\u54c1\u4e4b\u95f4\u7684\u5dee\u5f02\u500d\u6570\uff0c\u70b9\u8d8a\u504f\u79bb\u4e2d\u5fc3\uff0c\u8868\u793a\u5dee\u5f02\u500d\u6570\u8d8a\u5927\u3002\u706b\u5c71\u56fe\u7684\u7eb5\u8f74\u4e00\u822c\u662f -Log 10 (P-value) \uff0c\u8868\u793a\u5dee\u5f02\u662f\u5426\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\uff0c\u70b9\u8d8a\u9760\u56fe\u7684\u9876\u90e8\u8868\u793a\u5dee\u5f02\u8d8a\u663e\u8457\u3002\u706b\u5c71\u56fe\u7684\u70b9\u7684\u989c\u8272\u548c\u5927\u5c0f\u4e5f\u53ef\u4ee5\u8868\u793a\u66f4\u591a\u7684\u5c5e\u6027\uff0c\u5982\u57fa\u56e0\u7684\u4e0a\u8c03\u3001\u4e0b\u8c03\u3001\u65e0\u5dee\u5f02\u3001\u8868\u8fbe\u4e30\u5ea6\u7b49\u3002\u706b\u5c71\u56fe\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5feb\u901f\u7b5b\u9009\u51fa\u5177\u6709\u751f\u7269\u5b66\u610f\u4e49\u7684\u5dee\u5f02\u57fa\u56e0\uff0c\u5e76\u5728\u56fe\u4e0a\u6807\u8bb0\u51fa\u6765\u3002<\/p>\n

\u4ecb\u7ecd\u5b8c\u4e86\u706b\u5c71\u56fe\uff0c\u4e3a\u4e86\u5c0f\u4f19\u4f34\u4eec\u66f4\u52a0\u5168\u9762\u7684\u8ba4\u8bc6\u706b\u5c71\u56fe\uff0c\u4e0b\u9762\u5c0f\u679c\u8bf4\u4e00\u4e0b\u5b83\u7684\u4f18\u7f3a\u70b9\u3002<\/p>\n

\u706b\u5c71\u56fe\u7684\u4f18\u70b9\uff1a<\/p>\n

    \n
  1. \u5b83\u53ef\u4ee5\u5feb\u901f\u76f4\u89c2\u5730\u5c55\u793a\u51fa\u53d8\u5316\u5e45\u5ea6\u8f83\u5927\u4e14\u5177\u6709\u7edf\u8ba1\u5b66\u610f\u4e49\u7684\u6570\u636e\u70b9\uff0c\u5982\u5dee\u5f02\u57fa\u56e0\u7b49<\/li>\n
  2. \u5b83\u53ef\u4ee5\u5728\u56fe\u4e0a\u6807\u8bb0\u51fa\u5173\u6ce8\u7684\u57fa\u56e0\u7684\u540d\u5b57\uff0c\u65b9\u4fbf\u540e\u7eed\u7684\u5206\u6790\u548c\u9a8c\u8bc1<\/li>\n
  3. \u5b83\u53ef\u4ee5\u7528\u70b9\u7684\u989c\u8272\u548c\u5927\u5c0f\u8868\u793a\u66f4\u591a\u7684\u5c5e\u6027\uff0c\u5982\u57fa\u56e0\u7684\u4e0a\u8c03\u3001\u4e0b\u8c03\u3001\u8868\u8fbe\u4e30\u5ea6\u7b49<\/li>\n<\/ol>\n

    \u706b\u5c71\u56fe\u7684\u7f3a\u70b9\uff1a<\/p>\n

      \n
    1. \u5b83\u53ea\u9002\u5408\u5c55\u793a\u4e24\u7ec4\u6837\u54c1\u4e4b\u95f4\u7684\u6bd4\u8f83\uff0c\u4e0d\u80fd\u5c55\u793a\u591a\u7ec4\u6837\u54c1\u4e4b\u95f4\u7684\u5dee\u5f02<\/li>\n
    2. \u5b83\u4e0d\u80fd\u5c55\u793a\u6570\u636e\u70b9\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u6216\u805a\u7c7b\u60c5\u51b5\uff0c\u9700\u8981\u7ed3\u5408\u5176\u4ed6\u56fe\u5f62\u5982\u70ed\u56fe\u7b49<\/li>\n
    3. \u5b83\u53ef\u80fd\u53d7\u5230\u6570\u636e\u6807\u51c6\u5316\u3001\u6279\u6b21\u6548\u5e94\u7b49\u56e0\u7d20\u7684\u5f71\u54cd\uff0c\u5bfc\u81f4\u6570\u636e\u5b58\u5728\u7cfb\u7edf\u504f\u5dee<\/li>\n<\/ol>\n

      \u4efb\u4f55\u4e8b\u7269\u90fd\u4e0d\u4f1a\u662f\u5341\u5168\u5341\u7f8e\u7684\uff0c\u706b\u5c71\u56fe\u4e5f\u662f\u5982\u6b64\u3002\u4e0d\u8fc7\u6211\u4eec\u66f4\u5173\u6ce8\u5b83\u7684\u4f18\u70b9\u3002\u4e0b\u9762\u5c0f\u679c\u5e26\u5927\u5bb6\u4f7f\u7528ggplot2\u5305\u6765\u753b\u51fa\u7f8e\u89c2\u7684\u706b\u5c71\u56fe<\/p>\n

      \u9996\u5148\u662f\u6570\u636e\u5c55\u793a\uff0c\u524d\u5341\u884c\u7684\u6570\u636e\u5982\u4e0b\u56fe\u6240\u793a<\/p>\n

      <\/p>\n

      \u4e0b\u9762\u5c31\u662f\u4ee3\u7801\u90e8\u5206\u5566<\/p>\n

      rm( list = ls())<\/p>\n

      gc()<\/p>\n

      # \u8bbe\u7f6e\u5de5\u4f5c\u8def\u5f84<\/p>\n

      setwd(‘\/media\/desk16\/iyun010’)<\/p>\n

      library(tidyverse)<\/p>\n

      # \u8bfb\u53d6\u6570\u636e\u96c6<\/p>\n

      data <- read.csv(‘data.csv’)<\/p>\n

      # \u5c06p\u503c\u8fdb\u884c-log10\u8f6c\u5316<\/p>\n

      volc_plot <- ggplot(data, aes(LogFC, -log10(PValue))) +<\/p>\n

      geom_point(size = 0.4) + # \u8c03\u6574\u70b9\u7684\u5927\u5c0f<\/p>\n

      xlab(expression(“log”[2]*” fold change”)) + # \u4fee\u9970\u6a2a\u5750\u6807\u7684\u9898\u76ee<\/p>\n

      ylab(expression(“-log”[10]*” p-value”)) + # \u4fee\u9970\u7eb5\u5750\u6807\u7684\u9898\u76ee<\/p>\n

      scale_x_continuous(limits = c(-15, 15)) + # \u8c03\u6574\u6a2a\u5750\u6807\u7684\u8303\u56f4<\/p>\n

      theme_minimal()<\/p>\n

      data1 <- data %>%<\/p>\n

      mutate(expression = case_when(LogFC >= 1 & PValue < 0.05 ~ “Up-regulated”, # \u4e0a\u8c03<\/p>\n

      LogFC <= -1 & PValue < 0.05 ~ “Down-regulated”, # \u4e0b\u8c03<\/p>\n

      TRUE ~ “Unchanged”)) # \u4e0d\u53d8<\/p>\n

      volc_plot1 <- ggplot(data1, aes(LogFC, -log10(PValue))) +<\/p>\n

      geom_point(size = 0.4, aes(color = expression)) + # \u6839\u636eexpression\u6c34\u5e73\u8fdb\u884c\u7740\u8272<\/p>\n

      xlab(expression(“log”[2]*” fold change”)) + # \u4fee\u9970x\u8f74\u9898\u76ee<\/p>\n

      ylab(expression(“-log”[10]*” p-value”)) + # \u4fee\u9970y\u8f74\u9898\u76ee<\/p>\n

      scale_x_continuous(limits = c(-15, 15)) +<\/p>\n

      scale_color_manual(values = c(“steelblue”, “grey”, “red”))+ # \u6dfb\u52a0\u4e09\u79cd\u989c\u8272<\/p>\n

      # theme_minimal<\/p>\n

      theme_bw() +<\/p>\n

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

      theme(axis.line = element_line(colour = “black”))<\/p>\n

      ggsave(‘volc.png’, plot = last_plot(),width=225, height =150,units = “mm” ,dpi=300)<\/p>\n

      \u753b\u51fa\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff0c\u662f\u4e0d\u662f\u5f88\u7f8e\u89c2\u5462 \"volc\"<\/p>\n

      \u4eca\u5929\u7684\u706b\u5c71\u56fe\u7ed8\u5236\u6559\u7a0b\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\u54e6\uff0c\u6211\u4eec\u4e0b\u6b21\u89c1~<\/p>\n","protected":false},"excerpt":{"rendered":"

      \u706b\u5c71\u56fe\u76f8\u4fe1\u5927\u5bb6\u80af\u5b9a\u90fd\u4e0d\u964c\u751f\uff0c\u4f46\u662f\u600e\u4e48\u753b\u51fa\u7f8e\u89c2\u800c\u53c8\u5927\u65b9\u7684\u706b\u5c71\u56fe\u53ef\u8ba9\u5f88\u591a\u5c0f\u4f19\u4f34\u6293\u8033\u6320\u816e\u4e86\uff0c\u4e0b\u9762\u5c0f\u679c\u5316\u8eab\u8001\u53f8\u673a\u5e26\u5c0f\u4f19 […]<\/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\/23705"}],"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=23705"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23705\/revisions"}],"predecessor-version":[{"id":23708,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23705\/revisions\/23708"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23705"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23705"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23705"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}