{"id":30179,"date":"2024-02-28T18:06:38","date_gmt":"2024-02-28T10:06:38","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30179"},"modified":"2024-02-28T18:06:39","modified_gmt":"2024-02-28T10:06:39","slug":"r%e8%af%ad%e8%a8%80%e5%b8%a6%e4%bd%a0%e6%8e%a2%e7%b4%a2%e5%8d%95%e7%bb%86%e8%83%9e%e8%a1%a8%e5%9e%8b%e4%bf%a1%e6%81%af","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30179","title":{"rendered":"R\u8bed\u8a00\u5e26\u4f60\u63a2\u7d22\u5355\u7ec6\u80de\u8868\u578b\u4fe1\u606f"},"content":{"rendered":"<p><strong>R\u8bed\u8a00\u5e26\u4f60\u63a2\u7d22\u5355\u7ec6\u80de\u8868\u578b\u4fe1\u606f<\/strong><\/p>\n<p>\u4eca\u5929\uff0c\u5c0f\u679c\u8981\u5e26\u5927\u5bb6\u7ee7\u7eed\u63a2\u7d22\u5355\u7ec6\u80de\u6d4b\u5e8f\u76f8\u5173R\u5305\u7684\u5b66\u4e60\u3002\u4e4b\u524d\u4e3a\u6211\u4eec\u5b66\u4e60\u4e86scRNAseq\u5305\u7684\u5b89\u88c5\u548c\u7b80\u5355\u4f7f\u7528\uff0c\u90a3\u4f60\u77e5\u9053\u5982\u4f55\u4f7f\u7528\u5b83\u4eec\u5e76\u5c55\u793a\u6bcf\u4e2a\u7ec6\u80de\u57fa\u672c\u7684\u8868\u578b\u4fe1\u606f\u5417\u3002\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/p>\n<ul>\n<li><strong>scRNAseq\u5305\u4e2d\u6709\u54ea\u4e9b\u6570\u636e\uff1f<\/strong><\/li>\n<\/ul>\n<p>\u9996\u5148\uff0cscRNAseq\u5305\u4e2d\u5b58\u653e\u7684\u662f\u4eba\u7c7b\u5355\u7ec6\u80de\u7ec6\u80de\uff0c\u5e76\u5c06\u5176\u5206\u4e3a\u56db\u7c7b\u7ec6\u80de\uff0c\u8fd9\u56db\u7c7b\u7ec6\u80de\u5206\u522b\u662f\uff1a<\/p>\n<ol>\n<li>neural progenitor cell (\u7531pluripotent stem cells\u5206\u5316\u800c\u6210)<\/li>\n<li>GW16<\/li>\n<li>GW21<\/li>\n<li>GW21+3 \uff08\u5b55\u671f\u7ec6\u80de\uff09<\/li>\n<\/ol>\n<p>\u5982\u679c\u60f3\u8981\u6df1\u5165\u4e86\u89e3\u8fd9\u4e9bR\u5305\uff0c\u540c\u5b66\u4eec\u53ef\u4ee5\u81ea\u884c\u67e5\u9605\u8d44\u6599\u4e86\u89e3\uff0c\u4f46\u5982\u679c\u662f\u504f\u6280\u672f\u5f00\u53d1\u7684\u540c\u5b66\u4e5f\u53ef\u4ee5\u8df3\u8fc7\u8fd9\u4e00\u90e8\u5206\u7684\u4ecb\u7ecd\u54e6\uff0c\u6211\u4eec\u76f4\u63a5\u8fdb\u5165\u4e0b\u9762\u7684\u6b63\u9898\u3002\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/p>\n<ul>\n<li><strong>\u6570\u636e\u8f7d\u5165<\/strong><\/li>\n<\/ul>\n<p>\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5e26\u5927\u5bb6\u4e00\u8d77\u901a\u8fc7scRNAseq\u5305\u6765\u5bfc\u5165\u6570\u636e\u3002<\/p>\n<p>library(scRNAseq)<br \/>\ndata(fluid) #\u521b\u5efa\u6570\u636e\u6d41\u540d\u79f0<br \/>\nfluid&lt;-ReprocessedFluidigmData() #\u4ecescRNAseq\u4e2d\u5bfc\u5165\u6570\u636e<br \/>\nct &lt;- floor(assays(fluid)$rsem_counts)<br \/>\nct[1:4,1:4]<br \/>\nsample &lt;- as.data.frame(colData(fluid))<br \/>\nDT::datatable(sample)<\/p>\n<p><strong><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"298\" class=\"wp-image-30180\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=640%2C298\" alt=\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?w=1927 1927w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=300%2C140 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=1024%2C477 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=768%2C357 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=1536%2C715 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?resize=600%2C279 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-114.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/strong> \u73b0\u5728\u8ba9\u6211\u4eec\u4e00\u8d77\u770b\u4e00\u4e0b\u5bfc\u5165\u540e\u7684\u6570\u636e\u77e9\u9635\u5427\uff01<\/p>\n<ul>\n<li><strong>\u6570\u636e\u7684\u8868\u578b\u4fe1\u606f<\/strong><\/li>\n<\/ul>\n<p>\u5728\u4e0a\u9762\u7684\u63cf\u8ff0\u4e2d\u63d0\u5230\uff0cscRNAseq\u5305\u4e2d\u5c06\u4eba\u7c7b\u5355\u7ec6\u80de\u5206\u4e3a\u56db\u5927\u7c7b\u7ec6\u80de\uff0c\u672c\u6b21\u5b9e\u9a8c\u7684\u6570\u636e\u96c6\u6765\u81ea130\u4e2a\u6570\u636e\u5e93\uff0c\u5176\u4e2d\u6bcf\u4e2a\u7ec6\u80de\u7684\u6d4b\u5e8f\u6df1\u5ea6\u5747\u4e0d\u540c\uff0c\u90a3\u4e48\u6211\u4eec\u600e\u4e48\u80fd\u76f4\u89c2\u7684\u770b\u5230\u6bcf\u4e2a\u7ec6\u80de\u7684\u5177\u4f53\u7edf\u8ba1\u6307\u6807\u5462\uff1f\u63a5\u4e0b\u6765\u5c0f\u679c\u7528ggplot\u4e2d\u7684\u7bb1\u7ebf\u56fe\u6765\u7ed9\u5927\u5bb6\u5c55\u793a\u4e00\u4e0b\uff01<\/p>\n<p>library(ggplot2)<br \/>\nbox &lt;- lapply(colnames(sample_ann[,1:19]), function(i){<br \/>\ndat &lt;- sample_ann[,i,drop=F]<br \/>\ndat$sample=rownames(dat)<br \/>\n##\u7ed8\u5236boxplot<br \/>\nggplot(dat,aes(&#8216;all cells&#8217;,get(i)))+<br \/>\ngeom_boxplot()+<br \/>\nxlab(NULL)+ylab(i)<br \/>\n})<br \/>\nplot_grid(plotlist=box,ncol=5)<\/p>\n<p>\u6ce8\u610f\u5566\uff01\u6700\u540e\u53ef\u89c6\u5316\u7684plot_grid()\u51fd\u6570\u6765\u81eacowplot\u5305\u54e6\uff0c\u540c\u5b66\u4eec\u9700\u8981\u63d0\u524d\u4e0b\u8f7d\u5e76\u5bfc\u5165\u54e6\uff0c\u4e0d\u7136\u6700\u540e\u4e00\u5b9a\u4f1a\u62a5\u9519\uff01<\/p>\n<p>\u73b0\u5728\u8ba9\u6211\u4eec\u4e00\u8d77\u770b\u770b\u7ed3\u679c\u5427\uff1a <img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"469\" class=\"wp-image-30181\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=640%2C469\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?w=2500 2500w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=300%2C220 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=1024%2C750 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=768%2C562 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=1536%2C1125 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=2048%2C1500 2048w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?resize=600%2C439 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-2.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<ul>\n<li>\n<ul>\n<li><strong>\u9700\u8981\u6ce8\u610f\u7684\u5c0f\u95ee\u9898\uff1a<\/strong><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"87\" class=\"wp-image-30182\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-3.png?resize=640%2C87\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-3.png?w=932 932w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-3.png?resize=300%2C41 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-3.png?resize=768%2C105 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30179-3.png?resize=600%2C82 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u5c0f\u679c\u5728\u4e00\u5f00\u59cb\u8fdb\u884c\u53ef\u89c6\u5316\u7684\u65f6\u5019\uff0c\u7cfb\u7edf\u62a5\u9519\uff1a<\/p>\n<p>\u56e0\u4e3a\u60f3\u5230\u540c\u5b66\u4eec\u4e5f\u53ef\u80fd\u548c\u5c0f\u679c\u72af\u540c\u6837\u7684\u9519\u8bef\uff0c\u6240\u4ee5\u5c0f\u679c\u5728\u8fd9\u91cc\u5148\u7ed9\u5927\u5bb6\u505a\u4e2a\u9884\u9632\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"205\" class=\"wp-image-30183\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-115.png?resize=640%2C205\" alt=\"\u56fe\u5f62\u7528\u6237\u754c\u9762, \u5e94\u7528\u7a0b\u5e8f\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-115.png?w=796 796w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-115.png?resize=300%2C96 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-115.png?resize=768%2C246 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-115.png?resize=600%2C192 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u5176\u5b9e\u8fd9\u4e0d\u662f\u4ec0\u4e48\u5f88\u5927\u7684\u95ee\u9898\uff0c\u5982\u679c\u7ecf\u5e38\u7528R\u5de5\u5177\u5305\u753b\u56fe\uff0c\u5c31\u53ef\u80fd\u4f1a\u62a5\u8fd9\u6837\u7684\u9519\u8bef\u54e6\uff0c\u6240\u4ee5\u53ea\u8981\u4e3a\u6211\u4eec\u628a\u540e\u53f0\u7684\u56fe\u7247\u7f13\u5b58\u8fdb\u884c\u6e05\u7406\u5373\u53ef\u89e3\u51b3!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>R\u8bed\u8a00\u5e26\u4f60\u63a2\u7d22\u5355\u7ec6\u80de\u8868\u578b\u4fe1\u606f \u4eca\u5929\uff0c\u5c0f\u679c\u8981\u5e26\u5927\u5bb6\u7ee7\u7eed\u63a2\u7d22\u5355\u7ec6\u80de\u6d4b\u5e8f\u76f8\u5173R\u5305\u7684\u5b66\u4e60\u3002\u4e4b\u524d\u4e3a\u6211\u4eec\u5b66\u4e60\u4e86scRNAs [&hellip;]<\/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\/30179"}],"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=30179"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30179\/revisions"}],"predecessor-version":[{"id":30184,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30179\/revisions\/30184"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30179"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30179"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30179"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}