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none;\">\u76ee\u524d\u8bb8\u591a\u7684\u751f\u4fe1\u5206\u7ec4\u867d\u7136\u4ed6\u4eec\u7ecf\u5e38\u4f1a\u505aPCA\u5206\u6790\uff0c\u4f46\u662f\u4ed6\u4eec\u90fd\u662f\u5f88\u666e\u901a\u7684\u53ef\u89c6\u5316\u65b9\u5f0f\uff0c\u6700\u591a\u7684\u5c31\u662f\u6a2a\u7eb5\u5750\u6807\u7684PCA\u4e8c\u7ef4\u56fe\uff0c\u518d\u8005\u5c31\u662f\u4e09\u7ef4\u7684PCA\u56fe\u3002\u5c0f\u679c\u60f3\u6559\u7ed9\u5c0f\u4f19\u4f34\u4e0d\u4e00\u6837\u65b9\u5f0f\u7684PCA\u56fe\uff0c\u7136\u540e\u5c31\u53d1\u73b0\u4e00\u7bc7Nature\u6587\u7ae0\u4e2d\u7684PCA\u56fe\uff0c\u8fd9\u5e45\u56fe\u6253\u7834\u6b63\u5e38\u6211\u4eec\u89c1\u8fc7\u7684PCA\u56fe\uff0c\u6211\u4eec\u5148\u770b\u56fe\u5728\u4e86\u89e3\u4e00\u4e0b\u8fd9\u4e2a\u56fe\u7684\u7279\u8272\uff0c\u8fd9\u662f\u6765\u81eaIF\u5f71\u54cd\u56e0\u5b50\u670946.9\u300aNatue biotechnology\u300b\u4e2d\u7684\u300a<\/span><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(34, 34, 34);\">Removing unwanted variation from large-scale RNA sequencing data with PRPS\u300b\u56fe2a\uff0c\u6765\u770b\u4e00\u4e0b\uff1a<\/span><\/span><\/p>\n<p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014826\" data-ratio=\"0.4583333333333333\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ZclQaMTbJTGqJ9BZrpnsQX41a9Cicg.png?resize=640%2C293\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGUjvkxHzbibiaMzbLib6C5oNtNCUAZclQaMTbJTGqJ9BZrpnsQX41a9Cicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"293 .030029296875\" width=\"640 .5800170898438\" data-recalc-dims=\"1\" \/><\/span><span style=\"font-size: 16px;\">    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"> \u5c0f\u4f19\u4f34\u770b\u7684\u7b2c\u4e00\u773c\u662f\u4e0d\u662f\u89c9\u5f97\u8fd9\u4e0d\u662fPCA\u56fe\uff0c\u5c0f\u679c\u4e5f\u662f\u7b2c\u4e00\u773c\u5c31\u88ab\u5438\u5f15\u4e86\uff0c\u8fd9\u5e45\u56fe\uff0cPCA\u4e3b\u8981\u7684\u5185\u5bb9\u5e94\u6709\u5c3d\u6709\uff0c\u5e76\u4e14\u8fd8\u975e\u5e38\u7684\u597d\u770b\uff0c\u90a3\u4e48\u4eca\u5929\u5c0f\u679c\u5c31\u5e26\u5c0f\u4f19\u4f34\u53bb\u590d\u73b0\u8fd9\u5f20\u56fe\uff0c\u6211\u4eec\u4ee5\u540e\u505aPCA\u5c31\u53ef\u4ee5\u7528\u5230\u8fd9\u79cd\u56fe\u4e86\uff0c<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u4f5c\u56fe\u7684\u524d\u63d0\u5462\uff0c\u5c0f\u679c\u8fd8\u662f\u5e26\u5c0f\u4f19\u4f34\u4e86\u89e3\u4e00\u4e0b\u4ec0\u4e48\u662fPCA\uff0c\u6211\u4eec\u4e5f\u8981\u660e\u767d\u4e3a\u4ec0\u4e48\u8981\u505a\u8fd9\u4e2a\u56fe\uff0c\u5176\u5b9e\u4e3b\u6210\u5206\u5206\u6790\u5c5e\u4e8e\u4e00\u79cd\u964d\u7ef4\u7b97\u6cd5\uff0c\u5f53\u6211\u4eec\u7684\u6570\u636e\u91cf\u5f88\u5e9e\u5927\u7684\u65f6\u5019\u5c31\u9700\u8981\u53bb\u628a\u6570\u636e\u964d\u7ef4\uff0c\u800c\u964d\u7ef4\u5462\u5c31\u662f\u4e00\u79cd\u5bf9\u9ad8\u7ef4\u5ea6\u7279\u5f81\u6570\u636e\u9884\u5904\u7406\u65b9\u6cd5\u3002\u964d\u7ef4\u662f\u5c06\u9ad8\u7ef4\u5ea6\u7684\u6570\u636e\u4fdd\u7559\u4e0b\u6700\u91cd\u8981\u7684\u4e00\u4e9b\u7279\u5f81\uff0c\u53bb\u9664\u566a\u58f0\u548c\u4e0d\u91cd\u8981\u7684\u7279\u5f81\uff0c\u4ece\u800c\u5b9e\u73b0\u63d0\u5347\u6570\u636e\u5904\u7406\u901f\u5ea6\u7684\u76ee\u7684\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5728\u5b9e\u9645\u7684\u751f\u4ea7\u548c\u5e94\u7528\u4e2d\uff0c\u964d\u7ef4\u5728\u4e00\u5b9a\u7684\u4fe1\u606f\u635f\u5931\u8303\u56f4\u5185\uff0c\u53ef\u4ee5\u4e3a\u6211\u4eec\u8282\u7701\u5927\u91cf\u7684\u65f6\u95f4\u548c\u6210\u672c\u3002\u964d\u7ef4\u4e5f\u6210\u4e3a\u5e94\u7528\u975e\u5e38\u5e7f\u6cdb\u7684\u6570\u636e\u9884\u5904\u7406\u65b9\u6cd5\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u4e48\u505a\u662f\u6709\u5229\u4e8e\u6211\u4eec\u5206\u6790\u7684\uff0c\u53ef\u4ee5\u4f7f\u5f97\u6570\u636e\u96c6\u66f4\u6613\u4f7f\u7528\u3002\u4e5f\u53ef\u4ee5\u4f7f\u5f97\u7ed3\u679c\u5bb9\u6613\u7406\u89e3\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u90a3\u4e48\u8bdd\u4e0d\u591a\u8bf4\uff0c\u6211\u4eec\u5c31\u5f00\u59cb\u4e0b\u9762\u7684\u5b66\u4e60\u5427\uff01<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 16px;\">\u8fd9\u91cc\u5462\u5c0f\u679c\u8fd8\u8981\u8bf4\u660e\u4e00\u4e0b\uff0c\u6211\u4eec\u505aPCA\uff0c\u6570\u636e\u5e93\u5f88\u5927\u7684\u8bdd\uff0c\u90a3\u4e48\u6211\u4eec\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u6240\u4ee5\u5efa\u8bae\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ef\u4ee5\u4f7f\u7528\u670d\u52a1\u5668\u53bb\u8fd0\u884c\uff0c\u5982\u679c\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\u4e5f\u6ca1\u6709\u5173\u7cfb\uff0c\u53ef\u4ee5\u6b22\u8fce\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u670d\u52a1\u5668\u79df\u8d41~<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-size: 16px;text-indent: 0em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014835\" data-ratio=\"0.38981481481481484\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-14.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png&wxfrom=5&wx_lazy=1&wx_co=1'\" data-w=\"1080\" data-recalc-dims=\"1\" \/>\u597d\u4e86\uff0c\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u6211\u4eec\u5728\u505aPCA\u5206\u6790\u7684\u65f6\u5019\uff0c\u56e0\u4e3a\u5bf9\u8bb8\u591a\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u8fd9\u5c31\u9700\u8981\u7528\u5230\u4e00\u4e9b\u51fd\u6570\u53bb\u8ba1\u7b97\uff0c<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u6b21\u5c0f\u679c\u5c31\u5206\u4eab\u7ed9\u5c0f\u4f19\u4f34\u4e24\u4e2a\u51fd\u6570\uff0c\u6765\u5b9e\u73b0\u6211\u4eec\u8fd9\u6b21\u7684\u590d\u73b0\u5185\u5bb9\uff0c<\/span><\/p>\n<p style=\"text-indent: 0em;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u7b2c\u4e00\u4e2a\u5c31\u662f\u6211\u4eec\u7528\u6765\u8ba1\u7b97\u4e3b\u6210\u5206\u5206\u6790\u7684pca\u51fd\u6570<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\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=\"php\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">.pca <- function(data, is.log) {<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if (is.log)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> data <- data<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">else<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> data <- log2(data + 1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> svd <- base::svd(scale(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x = t(data),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> center = TRUE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale = FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> percent <- svd$d ^ 2 \/ sum(svd$d ^ 2) * 100<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> percent <-<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> sapply(seq_along(percent),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">function(i) {<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> round(percent[i], 1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> })<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">return(list(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> sing.val = svd,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> variation = percent))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\u8fd9\u4e2a\u51fd\u6570\u53ef\u4ee5\u8ba1\u7b97\u6211\u4eec\u7684\u6240\u6709\u7684\u6570\u636e\uff0c\u5c0f\u4f19\u4f34\u4e5f\u4e0d\u7528\u7406\u89e3\u8fd9\u4e2a\u51fd\u6570\u5177\u4f53\u610f\u601d\uff0c<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u7b2c\u4e8c\u4e2a\u51fd\u6570\u5c31\u662f\u7528\u6765\u4f5c\u56fe\u7684\uff0c\u8fd9\u4e2a\u5c31\u9700\u8981\u7528\u5230\u6211\u4eec\u7684\u8001\u670b\u53cbggplot2\u5305\u4e2d\u7684ggpubr\u8fd8\u6709cowplot\u5305\uff0c<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u6765\u770b\u4e00\u4e0b\uff1a<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\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=\"php\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">.scatter.density.pc <- function(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pcs, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pc.var, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group.name, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> color, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeSize, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pointSize, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeColor,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> title<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pair.pcs <- utils::combn(ncol(pcs), 2)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pList <- list()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for(i in 1:ncol(pair.pcs)){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if(i == 1){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x <- pair.pcs[1,i]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> y <- pair.pcs[2,i]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p <- ggplot(mapping = aes(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x = pcs[,x],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> y = pcs[,y],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fill = group)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> xlab(paste0('PC', x, ' (', pc.var[x], '%)')) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ylab(paste0('PC', y, ' (', pc.var[y], '%)')) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_point(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> aes(fill = group),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pch = 21,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> color = strokeColor,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> stroke = strokeSize,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> size = pointSize,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = alpha) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_x_continuous(breaks = scales::pretty_breaks(n = 5)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_y_continuous(breaks = scales::pretty_breaks(n = 5)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ggtitle(title) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.position = \"right\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> panel.background = element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.line = element_line(colour = \"black\", size = 1.1),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.background = element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.text = element_text(size = 12),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.title = element_text(size = 14),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.key = element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.x = element_text(size = 10),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.y = element_text(size = 10),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.title.x = element_text(size = 14),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.title.y = element_text(size = 14)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> guides(fill = guide_legend(override.aes = list(size = 4))) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_fill_manual(name = group.name, values = color)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> le <- ggpubr::get_legend(p)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }else{<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x <- pair.pcs[1,i]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> y <- pair.pcs[2,i]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p <- ggplot(mapping = aes(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x = pcs[,x],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> y = pcs[,y],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fill = group)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> xlab(paste0('PC', x, ' (',pc.var[x], '%)')) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ylab(paste0('PC', y, ' (',pc.var[y], '%)')) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_point(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> aes(fill = group),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pch = 21,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> color = strokeColor,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> stroke = strokeSize,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> size = pointSize,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = alpha) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_x_continuous(breaks = scales::pretty_breaks(n = 5)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_y_continuous(breaks = scales::pretty_breaks(n = 5)) + <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> panel.background = element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.line = element_line(colour = \"black\", size = 1.1),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> legend.position = \"none\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.x = element_text(size = 10),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.text.y = element_text(size = 10),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.title.x = element_text(size = 14),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis.title.y = element_text(size = 14)) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_fill_manual(values = color, name = group.name)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p <- p + theme(legend.position = \"none\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> xdens <- cowplot::axis_canvas(p, axis = \"x\")+<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_density(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mapping = aes(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x = pcs[,x],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fill = group),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = 0.7,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> size = 0.2<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(legend.position = \"none\") +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_fill_manual(values = color)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ydens <- cowplot::axis_canvas(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> axis = \"y\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> coord_flip = TRUE) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> geom_density(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mapping = aes(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> x = pcs[,y],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fill = group),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = 0.7,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> size = 0.2) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> theme(legend.position = \"none\") +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale_fill_manual(name = group.name, values = color) +<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> coord_flip()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p1 <- insert_xaxis_grob(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> xdens,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> grid::unit(.2, \"null\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> position = \"top\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> )<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p2 <- insert_yaxis_grob(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> p1, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> ydens,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> grid::unit(.2, \"null\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> position = \"right\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> )<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pList[[i]] <- ggdraw(p2)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pList[[i+1]] <- le<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">return(pList)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u5c0f\u4f19\u4f34\u53ef\u4ee5\u76f4\u63a5\u8fd0\u884c\u8fd9\u4e24\u4e2a\u51fd\u6570\uff0c\u6216\u8005\u4e5f\u53ef\u4ee5\u60f3\u5c0f\u679c\u4e00\u6837\u6574\u7406\u5728\u4e00\u4e2aR\u6587\u4ef6\u91cc\u9762\uff0c\u65b9\u4fbf\u4e0b\u6b21\u4f7f\u7528\uff0c<\/span><\/p>\n<p style=\"text-indent: 21pt;text-align: center;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014822\" data-ratio=\"1.0707070707070707\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_XOBM8OJ6lxd3MrSY2mS8f5hBgvUiaQ.png?resize=395%2C423\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGkkjibpXwsZ0KibTY5fJeBfyNVN9XOBM8OJ6lxd3MrSY2mS8f5hBgvUiaQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"396\" height=\"423 .95001220703125\" width=\"395 .96002197265625\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u7136\u540e\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528<\/span>    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">source(“pca.r”)#\u8f7d\u5165\u4f7f\u7528<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u4e0b\u9762\u6211\u4eec\u5c31\u662f\u6765\u770b\u4e0b\u8f7d\u5165\u6570\u636e\u7684\u683c\u5f0f\uff0c<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u662f\u5c0f\u56fe\u81ea\u5df1\u7684\u6570\u636e\uff0c\u5c0f\u4f19\u4f34\u53ef\u4ee5\u6309\u7167\u5f62\u5f0f\u81ea\u884c\u53bb\u8bbe\u7f6e\uff0c<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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=\"css\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">df<-read.csv(\"pca1.csv\" )<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\">df<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014824\" data-ratio=\"0.7954887218045112\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_4yRBznRia815nPbYHbWWMzCyrOpwVw.png?resize=553%2C440\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGYZcBuzGiaKt6WVVXWZaP8Rq9fq4yRBznRia815nPbYHbWWMzCyrOpwVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"665\" height=\"440 .5400085449219\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u6211\u4eec\u5c55\u793a\u6700\u91cd\u8981\u7684\u4e00\u90e8\u5206\uff0c\u524d\u9762\u90fd\u662f\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\uff0c\u7eb5\u7684\u8868\u793a\u6837\u672c\uff0c\u6700\u540e\u4e00\u4e2a\u6211\u4eec\u8bbe\u7f6e\u4e00\u4e0b\u5206\u7ec4\uff0c\u4f5c\u4e3a\u6211\u4eecPCA\u5206\u6790\u7684\u6570\u636e\u5f62\u5f0f\uff0c\u5c31\u662fClassification,\u5c0f\u56fe\u8fd9\u91cc\u5206\u4e86\u56db\u7ec4\uff0c\u6587\u732e\u4e2d\u5206\u4e865\u7ec4\uff0c\u8fd9\u4e2a\u770b\u5c0f\u4f19\u4f34\u81ea\u5df1\u7684\u9700\u6c42\uff0c<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u7136\u540e\u6211\u4eec\u8ba1\u7b97\u4e00\u4e0b<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pca.ncg<-.pca(data = df[,1:8767], ##<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">is.log = FALSE)<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"> <\/span><o:page><\/o:page><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u4e0a\u9762\u8fd9\u4e2a\u6570\u5b57\u4ee3\u8868\u57fa\u56e0\u6570\u91cf\uff0c\u5c0f\u56fe\u8fd9\u91cc\u5c31\u9009\u62e9\u8fd9\u4e00\u4e9b<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd0\u884c\u5b8c\u5c31<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014825\" data-ratio=\"0.07715582450832073\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_5OdRBbcGlTMtbBkicvaRKm4ylN1JsQ.png?resize=553%2C42\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGA7iaRHZntJJLzUDuzibL4QxQ9nq5OdRBbcGlTMtbBkicvaRKm4ylN1JsQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"661\" height=\"42 .66999816894531\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/>\u51fa\u73b0\uff0c\u6211\u4eec\u5c31\u5c06\u8ba1\u7b97\u597d\u7684\u503c\u8fdb\u884c\u53ef\u89c6\u5316\uff0c<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<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=\"php\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">.scatter.density.pc(pcs = pca.ncg$sing.val$v[, 1:3], ##\u5c55\u793a\u51e0\u4e2a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pc.var = pca.ncg$variation,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeColor = 'gray30',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeSize = .2,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pointSize = 2,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = .6,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> title = \"A\", ##\u6807\u9898\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group.name = \"Stage\", # legned name<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group=df$classification, # \u9009\u62e9\u5206\u7ec4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> color=c(\"darkorchid4\",\"cornflowerblue\",\"sandybrown\",\"mediumaquamarine\")) -> p#\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\u4e0b\u9762\u6211\u4eec\u4f7f\u7528\u4ee3\u7801\u8fdb\u884c\u5c55\u793a\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">do.call(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gridExtra::grid.arrange,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> c(p,ncol=4,nrow=1))<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014823\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_YTtyiahS32j83XSSpCbyib2uuFTb1Q.png?resize=553%2C553\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGBAJLOrDXm2Ria5zZbjyiala35GLzYTtyiahS32j83XSSpCbyib2uuFTb1Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"649\" height=\"553 .739990234375\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u6837\u4e00\u770b\uff0c\u548c\u6587\u732e\u4e2d\u6709\u70b9\u4e0d\u4e00\u6837\uff0c\u592a\u957f\u4e86\uff0c\u6211\u4eec\u628a\u51fa\u56fe\u7684\u6392\u5217\u6539\u4e00\u4e0b<\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">do.call(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gridExtra::grid.arrange,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> c(p,ncol=2,nrow=2))<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014827\" data-ratio=\"0.9833836858006042\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_7NdJzHNI9IKBEyxk6Mx8PL8E2icbAQ.png?resize=553%2C544\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGGibPb9JLl83LaVZFVAbPR5Bdye7NdJzHNI9IKBEyxk6Mx8PL8E2icbAQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"662\" height=\"544 .5399780273438\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u6837\u4e00\u6765\u5c31\u5dee\u4e0d\u591a\u4e86\uff0c\u6700\u540e\u518d\u628a\u70b9\u7684\u5927\u5c0f\u8c03\u4e00\u4e0b\uff0c\u7136\u540e\u51fa\u56fe\uff0c<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/p>\n<p style=\"text-indent:21.0pt;\"><br \/><\/p>\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<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=\"php\"><p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">.scatter.density.pc(pcs = pca.ncg$sing.val$v[, 1:3], ##<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pc.var = pca.ncg$variation,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeColor = 'gray30',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> strokeSize = .2,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> pointSize = 4,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> alpha = .6,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> title = \"A\", ## <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group.name = \"Stage\", # legned name<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> group=df$classification, #<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> color=c(\"darkorchid4\",\"cornflowerblue\",\"sandybrown\",\"mediumaquamarine\")) -> p<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">do.call(<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> gridExtra::grid.arrange,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> c(p,ncol=2,nrow=2))<\/span><\/span><\/code><\/p><\/pre>\n<\/section>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014828\" data-ratio=\"0.9923780487804879\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_ckGHriafpLL5nI5vQtCeY8GfUtqicA.png?resize=553%2C549\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwoicvOBiafjVyOT0qf8C9eGGJXd9gCaP5G59kZpnkVs3y75GwpckGHriafpLL5nI5vQtCeY8GfUtqicA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"656\" height=\"549 .5399169921875\" width=\"553 .739990234375\" data-recalc-dims=\"1\" \/><\/span><span style=\"font-size: 16px;\">    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">\u8fd9\u5c31\u4e00\u6837\u4e86\u57fa\u672c\u4e0a\u5c31\u4e00\u6837\u4e86\uff0c\u989c\u8272\u5c0f\u56fe\u5c31\u968f\u673a\u8bbe\u7f6e\u7684\uff0c\u5c0f\u4f19\u4f34\u770b\u4e86\u6709\u6ca1\u6709\u5fc3\u52a8\u4e86\uff0c\u8981\u591a\u591a\u7406\u89e3\u4ee3\u7801\u7684\u610f\u601d\uff0c\u4e0a\u8ff0\u51fd\u6570\u7684\u6587\u4ef6\u5462\uff0c\u5c0f\u4f19\u4f34\u9700\u8981\u7684\u53ef\u4ee5\u627e\u6211\u4eec\u516c\u4f17\u53f7\u9886\u53d6\u54e6<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 16px;\">\u6700\u540e\u5462\uff0c\u5c0f\u679c\u7ed9\u5c0f\u4f19\u4f34\u5e26\u4e2a\u5c0f\u798f\u5229\uff0c\u5982\u679c\u5c0f\u4f19\u4f34\u89c9\u5f97\u81ea\u5df1\u8fd0\u884c\u4ee3\u7801\u592a\u9ebb\u70e6\uff0c\u53ef\u4ee5\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\u54df\uff0c\u91cc\u9762\u6709\u6210\u719f\u7684\u4ee3\u7801\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u51fa\u60f3\u8981\u7684\u56fe\u5462\u3002\u8fd9\u662f\u6211\u4eec\u7684\u7f51\u5740<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);text-decoration: none;font-size: 16px;\">http:\/\/www.biocloudservice.com\/home.html<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 16px;\"> <\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 16px;\">\u591a\u591a\u5173\u6ce8\u6211\u4eec\u516c\u4f17\u53f7\uff0c\u4e00\u6765\u5b66\u751f\u4fe1\uff01<\/span><\/p>\n<p style=\"text-indent: 21pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;font-size: 16px;\">  <\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<p style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014830\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_VmRkv7tSNKliafDnsuFR7BoeDgBrww-2.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxPqeNQsFjm2HibIuSld9Nh9GicQSWhJwHjia5tEevQvDIebLErVmRkv7tSNKliafDnsuFR7BoeDgBrww\/640?wx_fmt=jpeg&from=appmsg'\" data-type=\"jpeg\" data-w=\"900\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\" data-recalc-dims=\"1\" \/><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-left: 0pt;letter-spacing: 0.578px;text-indent: 0pt;text-wrap: wrap;text-align: justify;font-size: 12pt;font-family: helvetica;color: rgb(0, 0, 0);break-after: auto;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014831\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_FbEg9fibwQicL8l2ExKOZZTmAHXabQ-7.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAx3HetBkB7aOGibFWKqibqIATyC4zFibzCgdrxFwRep6cDMLIbA0FbEg9fibwQicL8l2ExKOZZTmAHXabQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;caret-color: rgba(0, 0, 0, 0);\" data-recalc-dims=\"1\" \/><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;outline: 0px;font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;background-color: rgb(255, 255, 255);text-align: left;\">\n<section style=\"outline: 0px;font-size: 16px;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;outline: 0px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;outline: 0px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;outline: 0px;\">\n<section style=\"outline: 0px;display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;outline: 0px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;outline: 0px;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;outline: 0px;display: inline-block;vertical-align: top;color: rgb(0, 154, 68);\">\n<p style=\"outline: 0px;\"><span style=\"font-size: 16px;\"><strong style=\"outline: 0px;\">\u5f80\u671f\u63a8\u8350<\/strong><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"outline: 0px;text-align: justify;\">\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: 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