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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015\",\"time\":\"2023-05-18 19:01:03\",\"timeStamp\":\"1684407663\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247487772&idx=1&sn=a2f1a2dcdf930207f273e3adb89a4b06&chksm=cf7c81d9f80b08cfa4d9eb7901b3d436ce23a6eff46f8ecea42ec519452ac74d824799c60f5b#rd\" target=\"_blank\" rel=\"noopener\">Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-05-18 19:01:03<\/em><\/div>\n<p><content><\/p>\n<section data-role=\"outer\" label=\"edit by 135editor\">\n<section style=\"letter-spacing: 0.578px;font-size: 16px;\">\n<section>\n<section>\n<section>\n<section>\n<section>\n<section data-width=\"100%\" style=\"width: 100%;flex: 0 0 100%;opacity: 1;\">\n<section style=\"line-height: 1.8;\">\n<section>\n<section>\n<section style=\"margin-top: 10px;margin-bottom: 20px;display: flex;flex-flow: row nowrap;text-align: center;justify-content: center;\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 70%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70% !important;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 30%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 30% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;line-height: 0;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"162\" data-cropsely1=\"0\" data-cropsely2=\"162\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-49.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" style=\"height: 111px;vertical-align: middle;width: 111px;\" data-ratio=\"1\" data-w=\"400\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<section><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5404\u4f4d\u5c0f\u4f19\u4f34\u4eec\uff0c\u5927\u5bb6\u597d\u5440\uff0c\u6211\u662f\u4f60\u4eec\u7684\u8001\u670b\u53cb\u5c0f\u679c\uff0c\u6700\u8fd1\u5c0f\u679c\u5728\u5206\u6790\u5355\u7ec6\u80de\u6570\u636e\u65f6\u9047\u5230\u4e86\u4e00\u4e2a\u95ee\u9898\uff0c\u5728\u8fd9\u91cc\u548c\u5927\u5bb6\u5206\u4eab\u4e00\u4e0b\u5440\u3002<\/span><\/section>\n<\/li>\n<\/ul>\n<section>\n<section>\n<section><br \/><\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u9996\u5148\u5c0f\u679c\u4ece10x Genomics\u652f\u6301\u7f51\u7ad9\u4e0a\u7684\u4e00\u4e2a\u516c\u5f00\u6570\u636e\u96c6\u4e0b\u8f7dFASTQ\u6587\u4ef6\u3002\u8fd9\u662f\u6765\u81ea\u4eba\u7c7b\u5916\u5468\u8840\u5355\u4e2a\u6838\u7ec6\u80de(PBMC)\u76841,000\u4e2aPBMC\u6570\u636e\u96c6\uff0c\u5305\u62ec\u6dcb\u5df4\u7ec6\u80de\uff08T\u7ec6\u80de\u3001B\u7ec6\u80de\u548cNK\u6740\u4f24\u7ec6\u80de\uff09\u548c\u5355\u6838\u7ec6\u80de\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e0b\u8f7d\u4ee3\u7801\u4e3a\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">wget https:<span class=\"code-snippet__comment\">\/\/cf.10xgenomics.com\/samples\/cell-exp\/3.0.0\/pbmc_1k_v3\/pbmc_1k_v3_fastqs.tar<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u6b64\u6570\u636e\u96c6\u5927\u5c0f\u4e3a5.17G\uff0c\u4e0d\u662f\u5f88\u5927\uff0c\u5927\u6982\u51e0\u5206\u949f\u5c31\u53ef\u4ee5\u4e0b\u8f7d\u5b8c\u6210\u55bd\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e4b\u540e\u5bf9\u6b64\u538b\u7f29\u6587\u4ef6\u8fdb\u884c\u89e3\u538b\u3002\u56e0\u4e3a\u8fd9\u662f\u4e00\u4e2atar\u6587\u4ef6\u800c\u4e0d\u662ftar.gz\u6587\u4ef6\uff0c\u6240\u4ee5\u4e0d\u9700\u8981\u4f7f\u7528-z\u53c2\u6570\u6765\u63d0\u53d6\u5b83\u3002<\/p>\n<p style=\"white-space: normal;\">\u4ee3\u7801\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">tar -xvf pbmc_1k_v3_fastqs.tar<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u4f7f\u7528cellranger\u8fdb\u884c\u5b9a\u91cf\u540e\uff0c\u5f97\u5230\u4e09\u4e2a\u6587\u4ef6\u5939\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.05970149253731343\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_eQVQwhHVJk2l99EPfOmhxnD4Xdyf2A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNvFu2CLBbkp1z5iaiazelh5tSoGeQVQwhHVJk2l99EPfOmhxnD4Xdyf2A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"335\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\">\u5c0f\u679c\u4ee5\u6b64\u4e09\u4e2a\u6587\u4ef6\u5939\u4f5c\u4e3a\u8f93\u5165\u6587\u4ef6\uff0c\u8fdb\u884cseurat\u7684\u5206\u6790\u3002<\/p>\n<p style=\"white-space: normal;\">\u5728\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u65f6\u9047\u5230\u4e00\u4e2a\u95ee\u9898\uff0c\u6570\u636e\u7f29\u653e\u4e4b\u540e\u8fdb\u884cPCA\u7ebf\u6027\u964d\u7ef4\uff0c\u4ee3\u7801\u5982\u4e0b\uff0c\u51fa\u73b0\u4e0b\u56fe\u7684\u9519\u8bef\u3002<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6570\u636e\u7f29\u653e<\/span><\/code><code><span class=\"code-snippet_outer\">all.genes <- rownames(scdata)<\/span><\/code><code><span class=\"code-snippet_outer\">scdata <- ScaleData(scdata, features = all.genes)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">scdata<\/span><\/code><code><span class=\"code-snippet_outer\">scdata <- RunPCA(scdata, features = VariableFeatures(object = scdata))<\/span><\/code><code><span class=\"code-snippet_outer\">DimPlot(scdata, reduction = <span class=\"code-snippet__string\">\"pca\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.15817223198594024\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_o0NbRMQ9pUu1OefcADWJMUbVmKAVXA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNJ1SuibSicAOW21tAmaRjW6v9dDo0NbRMQ9pUu1OefcADWJMUbVmKAVXA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"569\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6211\u4eec\u53ef\u4ee5\u53d1\u73b0\uff0c\u4e3b\u8981\u95ee\u9898\u662fRunPCA\u8fc7\u7a0b\u51fa\u73b0\u9519\u8bef\uff0c\u5bfc\u81f4\u6d41\u7a0b\u4e2d\u65ad\u3002\u53d1\u73b0\u62a5\u9519\u63d0\u793a\uff1a\u6700\u5927\u7684npcs\u5fc5\u987b\u4e25\u683c\u9075\u5faa\u5c0f\u4e8e\u6700\u5c0f\u884c\u5217\u6570\u7684\u89c4\u5219\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.19285714285714287\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_GmicwFT0HsFj5YJOZ4bhrA77vVNTnQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNDCK1zxnE6ZBAibVdsdicE13Kc5VGmicwFT0HsFj5YJOZ4bhrA77vVNTnQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"560\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span 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14px;\">1.\u5728\u5b66\u4e60\u67d0\u4e2a\u8f6f\u4ef6\u6216\u8005\u67d0\u4e2a\u5305\u7684\u4f7f\u7528\u65f6\uff0c\u6211\u4eec\u53ef\u4ee5\u8be6\u7ec6\u67e5\u770b\u6bcf\u4e00\u4e2a\u51fd\u6570\u7684\u4f7f\u7528\u624b\u518c\uff0c\u4e86\u89e3\u51fd\u6570\u7684\u539f\u7406\u3001\u529f\u80fd\u4ee5\u53ca\u6bcf\u4e2a\u53c2\u6570\u7684\u4f5c\u7528\uff0c\u8fd9\u6837\u5728\u6211\u4eec\u4e4b\u540e\u5b9e\u9645\u64cd\u4f5c\u8fc7\u7a0b\u4e2d\u4e5f\u6bd4\u8f83\u65b9\u4fbf\u5feb\u6377\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">2.\u5728\u9047\u5230\u95ee\u9898\u65f6\uff0c\u6211\u4eec\u8981\u4ed4\u7ec6\u67e5\u770b\u62a5\u9519\u5185\u5bb9\uff0c\u6839\u636e\u62a5\u9519\u63d0\u793a\u627e\u5bfb\u7b54\u6848\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 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1.59em;\"><\/em><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 26%;max-width: 26% !important;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 100%;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.005281690140845\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_0WFLKBMicbm6iawtkrNrMxpSVU9GBQ-6.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN261llpmfF6btPBTUKkibEdnRz5Y0WFLKBMicbm6iawtkrNrMxpSVU9GBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"568\" data-width=\"100%\" style=\"vertical-align: inherit;width: 100%;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 62%;max-width: 62% !important;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u5fae\u4fe1\u53f7 | 18502195490<\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-top: 12px;padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u77e5\u4e4e | \u751f\u4fe1\u679c<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"letter-spacing: 0.578px;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015 \u751f\u4fe1\u679c 2023-05-18 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/58972"}],"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=58972"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58972\/revisions"}],"predecessor-version":[{"id":58978,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58972\/revisions\/58978"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58972"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58972"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58972"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":58972,"date":"2024-06-17T07:19:18","date_gmt":"2024-06-16T23:19:18","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58972"},"modified":"2024-06-17T07:19:18","modified_gmt":"2024-06-16T23:19:18","slug":"seurat-runpca%e6%8a%a5%e9%94%99%ef%bc%9f%e5%b0%8f%e6%9e%9c%e6%95%99%e5%a4%a7%e5%ae%b6%ef%bc%8c%e9%81%87%e5%88%b0%e6%8a%a5%e9%94%99%e4%b8%8d%e8%a6%81%e6%80%95","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58972","title":{"rendered":"Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015"},"content":{"rendered":"

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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015\",\"time\":\"2023-05-18 19:01:03\",\"timeStamp\":\"1684407663\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247487772&idx=1&sn=a2f1a2dcdf930207f273e3adb89a4b06&chksm=cf7c81d9f80b08cfa4d9eb7901b3d436ce23a6eff46f8ecea42ec519452ac74d824799c60f5b#rd\" target=\"_blank\" rel=\"noopener\">Seurat RunPCA\u62a5\u9519\uff1f\u5c0f\u679c\u6559\u5927\u5bb6\uff0c\u9047\u5230\u62a5\u9519\u4e0d\u8981\u6015<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-05-18 19:01:03<\/em><\/div>\n<p><content><\/p>\n<section data-role=\"outer\" label=\"edit by 135editor\">\n<section style=\"letter-spacing: 0.578px;font-size: 16px;\">\n<section>\n<section>\n<section>\n<section>\n<section>\n<section data-width=\"100%\" style=\"width: 100%;flex: 0 0 100%;opacity: 1;\">\n<section style=\"line-height: 1.8;\">\n<section>\n<section>\n<section style=\"margin-top: 10px;margin-bottom: 20px;display: flex;flex-flow: row nowrap;text-align: center;justify-content: center;\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 70%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70% !important;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 30%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 30% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;line-height: 0;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"162\" data-cropsely1=\"0\" data-cropsely2=\"162\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-49.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" style=\"height: 111px;vertical-align: middle;width: 111px;\" data-ratio=\"1\" data-w=\"400\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<section><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5404\u4f4d\u5c0f\u4f19\u4f34\u4eec\uff0c\u5927\u5bb6\u597d\u5440\uff0c\u6211\u662f\u4f60\u4eec\u7684\u8001\u670b\u53cb\u5c0f\u679c\uff0c\u6700\u8fd1\u5c0f\u679c\u5728\u5206\u6790\u5355\u7ec6\u80de\u6570\u636e\u65f6\u9047\u5230\u4e86\u4e00\u4e2a\u95ee\u9898\uff0c\u5728\u8fd9\u91cc\u548c\u5927\u5bb6\u5206\u4eab\u4e00\u4e0b\u5440\u3002<\/span><\/section>\n<\/li>\n<\/ul>\n<section>\n<section>\n<section><br \/><\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u9996\u5148\u5c0f\u679c\u4ece10x Genomics\u652f\u6301\u7f51\u7ad9\u4e0a\u7684\u4e00\u4e2a\u516c\u5f00\u6570\u636e\u96c6\u4e0b\u8f7dFASTQ\u6587\u4ef6\u3002\u8fd9\u662f\u6765\u81ea\u4eba\u7c7b\u5916\u5468\u8840\u5355\u4e2a\u6838\u7ec6\u80de(PBMC)\u76841,000\u4e2aPBMC\u6570\u636e\u96c6\uff0c\u5305\u62ec\u6dcb\u5df4\u7ec6\u80de\uff08T\u7ec6\u80de\u3001B\u7ec6\u80de\u548cNK\u6740\u4f24\u7ec6\u80de\uff09\u548c\u5355\u6838\u7ec6\u80de\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e0b\u8f7d\u4ee3\u7801\u4e3a\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">wget https:<span class=\"code-snippet__comment\">\/\/cf.10xgenomics.com\/samples\/cell-exp\/3.0.0\/pbmc_1k_v3\/pbmc_1k_v3_fastqs.tar<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u6b64\u6570\u636e\u96c6\u5927\u5c0f\u4e3a5.17G\uff0c\u4e0d\u662f\u5f88\u5927\uff0c\u5927\u6982\u51e0\u5206\u949f\u5c31\u53ef\u4ee5\u4e0b\u8f7d\u5b8c\u6210\u55bd\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e4b\u540e\u5bf9\u6b64\u538b\u7f29\u6587\u4ef6\u8fdb\u884c\u89e3\u538b\u3002\u56e0\u4e3a\u8fd9\u662f\u4e00\u4e2atar\u6587\u4ef6\u800c\u4e0d\u662ftar.gz\u6587\u4ef6\uff0c\u6240\u4ee5\u4e0d\u9700\u8981\u4f7f\u7528-z\u53c2\u6570\u6765\u63d0\u53d6\u5b83\u3002<\/p>\n<p style=\"white-space: normal;\">\u4ee3\u7801\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">tar -xvf pbmc_1k_v3_fastqs.tar<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 14px;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u4f7f\u7528cellranger\u8fdb\u884c\u5b9a\u91cf\u540e\uff0c\u5f97\u5230\u4e09\u4e2a\u6587\u4ef6\u5939\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.05970149253731343\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_eQVQwhHVJk2l99EPfOmhxnD4Xdyf2A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNvFu2CLBbkp1z5iaiazelh5tSoGeQVQwhHVJk2l99EPfOmhxnD4Xdyf2A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"335\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"white-space: normal;\">\u5c0f\u679c\u4ee5\u6b64\u4e09\u4e2a\u6587\u4ef6\u5939\u4f5c\u4e3a\u8f93\u5165\u6587\u4ef6\uff0c\u8fdb\u884cseurat\u7684\u5206\u6790\u3002<\/p>\n<p style=\"white-space: normal;\">\u5728\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u65f6\u9047\u5230\u4e00\u4e2a\u95ee\u9898\uff0c\u6570\u636e\u7f29\u653e\u4e4b\u540e\u8fdb\u884cPCA\u7ebf\u6027\u964d\u7ef4\uff0c\u4ee3\u7801\u5982\u4e0b\uff0c\u51fa\u73b0\u4e0b\u56fe\u7684\u9519\u8bef\u3002<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6570\u636e\u7f29\u653e<\/span><\/code><code><span class=\"code-snippet_outer\">all.genes <- rownames(scdata)<\/span><\/code><code><span class=\"code-snippet_outer\">scdata <- ScaleData(scdata, features = all.genes)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u964d\u7ef4<\/span><\/code><code><span class=\"code-snippet_outer\">scdata<\/span><\/code><code><span class=\"code-snippet_outer\">scdata <- RunPCA(scdata, features = VariableFeatures(object = scdata))<\/span><\/code><code><span class=\"code-snippet_outer\">DimPlot(scdata, reduction = <span class=\"code-snippet__string\">\"pca\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.15817223198594024\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_o0NbRMQ9pUu1OefcADWJMUbVmKAVXA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNJ1SuibSicAOW21tAmaRjW6v9dDo0NbRMQ9pUu1OefcADWJMUbVmKAVXA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"569\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u6211\u4eec\u53ef\u4ee5\u53d1\u73b0\uff0c\u4e3b\u8981\u95ee\u9898\u662fRunPCA\u8fc7\u7a0b\u51fa\u73b0\u9519\u8bef\uff0c\u5bfc\u81f4\u6d41\u7a0b\u4e2d\u65ad\u3002\u53d1\u73b0\u62a5\u9519\u63d0\u793a\uff1a\u6700\u5927\u7684npcs\u5fc5\u987b\u4e25\u683c\u9075\u5faa\u5c0f\u4e8e\u6700\u5c0f\u884c\u5217\u6570\u7684\u89c4\u5219\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.19285714285714287\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_GmicwFT0HsFj5YJOZ4bhrA77vVNTnQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNDCK1zxnE6ZBAibVdsdicE13Kc5VGmicwFT0HsFj5YJOZ4bhrA77vVNTnQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"560\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">npcs\u5fc5\u987b\u8981\u5c0f\u4e8e\u6700\u5c0f\u884c\u5217\u6570\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0bnpcs = 50\uff0cscdata\u67e5\u770b\u77e9\u9635\u884c\u5217\u6570\uff0c\u53d1\u73b0\u6700\u5c0f\u503c\u4e3a30\uff0c\u5c06\u5176\u6539\u4e3a29\u540e\uff0c\u53ef\u4ee5\u6210\u529f\u8fd0\u884c\u3002<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\">\u8fd9\u8fb9\u5c0f\u679c\u603b\u7ed3\u4e00\u4e0b\uff1a<\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 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