{"id":484,"date":"2023-06-25T02:39:40","date_gmt":"2023-06-25T02:39:40","guid":{"rendered":"https:\/\/yunshangtulv.com.cn\/?p=484"},"modified":"2023-06-25T02:39:40","modified_gmt":"2023-06-25T02:39:40","slug":"nature-communications%e5%9b%be%e7%89%87%e5%a4%8d%e7%8e%b0%e6%95%a3%e7%82%b9%e5%b0%8f%e6%8f%90%e7%90%b4%e5%9b%be%e8%9c%9c%e8%9c%82%e5%9b%be","status":"publish","type":"post","link":"https:\/\/yunshangtulv.com.cn\/?p=484","title":{"rendered":"nature communications\u56fe\u7247\u590d\u73b0\u6563\u70b9\u5c0f\u63d0\u7434\u56fe+\u871c\u8702\u56fe"},"content":{"rendered":"<p><span>\u5bf9\u8bfb\u53d6\u7684\u6570\u636e\u8fdb\u884c\u4e00\u4e9b\u7edf\u8ba1\u5206\u6790\uff0c\u5e76\u521b\u5efa\u4e00\u4e2a\u5305\u542bviolin\u56fe\u3001\u70b9\u5206\u5e03\u3001\u5e73\u5747\u503c\u7ebf\u548c\u8bef\u5dee\u7ebf\u7684ggplot2\u56fe\u8868\u3002<\/span><\/p>\n<p>\u5047\u8bbe\u6570\u636e\u5305\u62ec\u4e24\u4e2a\u4e3b\u8981\u5217: \"Treatment\" \u548c \"Integrated.density\"\u3002\"Treatment\" \u5217\u5305\u542b\u5206\u7c7b\u53d8\u91cf\uff0c\"Integrated.density\" \u5217\u5305\u542b\u4e00\u4e9b\u6570\u503c\u3002\u540c\u65f6\u5b58\u5728 \"Biological.replicate\" \u5217\u7528\u4e8e\u8868\u793a\u751f\u7269\u590d\u5236\u3002\u6211\u4eec\u5c06\u751f\u6210\u8fd9\u6837\u7684\u968f\u673a\u6570\u636e\u3002<\/p>\n<p>\u8fd9\u662f\u751f\u6210\u6a21\u62df\u6570\u636e\u7684R\u8bed\u8a00\u4ee3\u7801\uff1a<\/p>\n<pre class=\"corepress-code-pre\"><code>#\u751f\u6210\u6a21\u62df\u6570\u636e\r\nset.seed(123)\r\n\r\nTreatment &lt;- rep(c(\"Treatment1\", \"Treatment2\", \"Treatment3\"), each = 100)\r\nIntegrated.density &lt;- rnorm(length(Treatment), mean = rep(c(100, 200, 150), each = 100), sd = 20)\r\nBiological.replicate &lt;- rep(1:3, times = 100)\r\n\r\nA &lt;- data.frame(Treatment, Integrated.density, Biological.replicate)\r\n\r\n#\u6253\u5370\u524d\u51e0\u884c\u6570\u636e\r\nhead(A)\r\n<\/code><\/pre>\n<p><span>\u8fd0\u884c\u8fd9\u6bb5\u4ee3\u7801\u540e\uff0c\u4f60\u53ef\u4ee5\u770b\u5230\u7c7b\u4f3c\u8fd9\u6837\u7684\u8f93\u51fa\uff1a<\/span><\/p>\n<p>Treatment Integrated.density Biological.replicate<br \/>\n1 Treatment1 120.57578 1<br \/>\n2 Treatment1 90.63943 2<br \/>\n3 Treatment1 102.73857 3<br \/>\n4 Treatment1 89.12502 1<br \/>\n5 Treatment1 110.98337 2<br \/>\n6 Treatment1 90.02306 3<\/p>\n<p>&nbsp;<\/p>\n<p>\u5b8c\u6574\u4ee3\u7801<\/p>\n<pre class=\"corepress-code-pre\"><code>\r\n\r\n# \u8bbe\u5b9a\u5de5\u4f5c\u76ee\u5f55\r\nsetwd(\"\")\r\n\r\n# \u751f\u6210\u6a21\u62df\u6570\u636e\r\nset.seed(123)\r\n\r\nTreatment &lt;- rep(c(\"Treatment1\", \"Treatment2\", \"Treatment3\"), each = 100)\r\nIntegrated.density &lt;- rnorm(length(Treatment), mean = rep(c(100, 200, 150), each = 100), sd = 20)\r\nBiological.replicate &lt;- rep(1:3, times = 100)\r\n\r\nA &lt;- data.frame(Treatment, Integrated.density, Biological.replicate)\r\n\r\n# \u52a0\u8f7d\u6240\u9700\u7684\u5e93\r\nlibrary(ggplot2)\r\nlibrary(ggbeeswarm)\r\nlibrary(ggpubr)\r\nlibrary(dplyr)\r\n\r\n# \u8f6c\u5316 'Biological.replicate' \u5217\u4e3a\u56e0\u5b50\r\nA$Biological.replicate &lt;- as.factor(A$Biological.replicate)\r\n\r\n# \u521b\u5efa\u65b0\u7684\u6570\u636e\u6846B\uff0c\u5305\u542b\u6bcf\u4e2a\u5904\u7406\u7ec4\u7684\u7edf\u8ba1\u6570\u636e\r\n# \u8ba1\u7b97B\u7684\u6570\u636e\r\nB &lt;- A %&gt;% \r\n  group_by(Treatment) %&gt;% \r\n  summarise(upper = quantile(Integrated.density, 0.75),\r\n         lower = quantile(Integrated.density, 0.25),\r\n         mean = mean(Integrated.density),\r\n         median = median(Integrated.density),\r\n         sd = sd(Integrated.density))\r\n\r\n# \u521b\u5efa\u56fe\u5f62\r\np &lt;- ggplot(A, aes(x=Treatment, y=Integrated.density)) +\r\n  geom_violin(width = 0.8, fill = '#EDEDED', color = '#EDEDED') +\r\n  geom_quasirandom(aes(color = Biological.replicate), width = 0.4, size = 2.5, alpha = 0.7) +\r\n  scale_color_manual(name = 'Rep.', values = c('#FFD7A8','#F2A9A9','#BAB099'), labels = c('1','2','3')) +\r\n  theme_bw() +\r\n  labs(x=\" \", y='Integrated density', title = \"Integrated Density by Treatment\") +\r\n  theme(plot.title = element_text(hjust = 0.5),\r\n        axis.title.y = element_text(colour = 'black', size = 16),\r\n        axis.text = element_text(colour = 'black', size = 14),\r\n        axis.line = element_line(linewidth = 1),\r\n        legend.title = element_text(size = 14),\r\n        legend.text = element_text(size = 14)) +\r\n  guides(color=guide_legend(override.aes = list(size=4))) +\r\n  geom_errorbar(data = B, aes(ymin = lower, ymax = upper, y=mean), width = 0.2, size = 0.5) +\r\n  stat_summary(fun = \"mean\", geom = \"crossbar\", mapping = aes(ymin = ..y.., ymax = ..y..), width = 0.4, linewidth = 0.3) +\r\n  stat_summary(aes(fill = Biological.replicate), geom = \"point\", fun = mean, shape = 21, size = 6, stroke = 1.3) +\r\n  scale_fill_manual(values = c('#FFAF51','#E65454','#756233')) +\r\n  guides(fill = guide_legend(title = 'Mean'))\r\n\r\nprint(p)   # \u6253\u5370\u56fe\u5f62\r\n\r\n# \u4fdd\u5b58\u56fe\u5f62\u4e3aPDF\u683c\u5f0f\r\nggsave(filename = \"plot.pdf\", plot = p, width = 11, height = 8)\r\n\r\n# \u4fdd\u5b58\u6570\u636e\u4e3aCSV\u683c\u5f0f\r\nwrite.csv(A, \"A.csv\", row.names = FALSE)\r\nwrite.csv(B, \"B.csv\", row.names = FALSE)\r\n<\/code><\/pre>\n<p>\u4ee5\u4e0a\u4ee3\u7801\u5c06\u751f\u6210\u4e00\u4e2a\u5305\u542b\u5c0f\u63d0\u7434\u56fe\u3001\u5206\u5e03\u70b9\u3001\u5e73\u5747\u503c\u7ebf\u548c\u8bef\u5dee\u7ebf\u7684ggplot2\u56fe\u5f62\uff0c\u5e76\u4fdd\u5b58\u4e3aPDF\u6587\u4ef6\u3002\u540c\u65f6\uff0c\u5b83\u8fd8\u4f1a\u5c06\u539f\u59cb\u6570\u636eA\u548c\u7edf\u8ba1\u6570\u636eB\u4fdd\u5b58\u4e3aCSV\u6587\u4ef6\u3002<\/p>\n<p>\u5982\u679c\u60f3\u8981\u7528\u81ea\u5df1\u7684\u6570\u636e\u8fd0\u884c\u6b64\u4ee3\u7801\uff0c\u6570\u636e\u5e94\u8be5\u662f\u4e00\u4e2a\u5305\u542b\u4ee5\u4e0b\u5217\u7684CSV\u6587\u4ef6\uff1a'Treatment', 'Integrated.density', \u548c 'Biological.replicate'\u3002'Treatment' \u5217\u5305\u542b\u4e86\u5904\u7406\u7684\u7c7b\u522b\uff0c'Integrated.density' \u5217\u5305\u542b\u4e86\u5bf9\u5e94\u7684\u6570\u503c\uff0c\u800c 'Biological.replicate' \u5217\u5305\u542b\u4e86\u751f\u7269\u590d\u5236\u7684\u7f16\u53f7\u3002<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-1024x1020.png\" alt=\"\" width=\"1024\" height=\"1020\" class=\"alignnone size-large wp-image-485\" srcset=\"https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-1024x1020.png 1024w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-300x300.png 300w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-100x100.png 100w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-600x598.png 600w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-150x150.png 150w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547-768x765.png 768w, https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/06\/\u622a\u56fe_20230625103547.png 1368w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5bf9\u8bfb\u53d6\u7684\u6570\u636e\u8fdb\u884c\u4e00\u4e9b\u7edf\u8ba1\u5206\u6790\uff0c\u5e76\u521b\u5efa\u4e00\u4e2a\u5305\u542bviolin\u56fe\u3001\u70b9\u5206\u5e03\u3001\u5e73\u5747\u503c\u7ebf\u548c\u8bef\u5dee\u7ebf\u7684ggplot2\u56fe\u8868\u3002 \u5047 [&hellip;]<\/p>\n","protected":false},"author":111,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9],"tags":[],"class_list":["post-484","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts\/484","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/users\/111"}],"replies":[{"embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=484"}],"version-history":[{"count":0,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts\/484\/revisions"}],"wp:attachment":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=484"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=484"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=484"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}