{"id":58492,"date":"2024-06-16T23:05:24","date_gmt":"2024-06-16T15:05:24","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58492"},"modified":"2024-06-16T23:06:35","modified_gmt":"2024-06-16T15:06:35","slug":"%e6%80%8e%e6%a0%b7%e8%bf%88%e5%87%ba%e7%b2%be%e5%87%86%e5%8c%bb%e5%ad%a6%e5%88%86%e6%9e%90%e7%ac%ac%e4%b8%80%e6%ad%a5%ef%bc%9fxeva%e5%b8%ae%e4%bd%a0%e6%89%93%e5%a5%bd%e8%8d%af%e7%89%a9%e9%9d%b6-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58492","title":{"rendered":"\u600e\u6837\u8fc8\u51fa\u7cbe\u51c6\u533b\u5b66\u5206\u6790\u7b2c\u4e00\u6b65\uff1fXeva\u5e2e\u4f60\u6253\u597d\u836f\u7269\u9776\u5411\u7684\u57fa\u7840\uff01"},"content":{"rendered":"<p><a style=\"font-size: revert; font-weight: revert;\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247498892&amp;idx=1&amp;sn=081cc06ad560fecacd1f762a1cf8290d&amp;chksm=cf7f6c49f808e55f6cc7332531a9c07f6435a624d5c042c12591b564948b4e168986d0c2d276#rd\" target=\"_blank\" rel=\"noopener\">\u600e\u6837\u8fc8\u51fa\u7cbe\u51c6\u533b\u5b66\u5206\u6790\u7b2c\u4e00\u6b65\uff1fXeva\u5e2e\u4f60\u6253\u597d\u836f\u7269\u9776\u5411\u7684\u57fa\u7840\uff01<\/a><\/p>\n<div class=\"rich_media\">\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b\u00a0\u00a0<\/span><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c\u00a0\u00a0<\/span><span id=\"profileBt\" class=\"rich_media_meta rich_media_meta_nickname\"><a id=\"js_name\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\"><\/a>\u751f\u4fe1\u679c\u00a0\u00a0<\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2024-01-18 19:00:43<\/em><\/div>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><a title=\"\u751f\u4fe1\u7ed8\u56fe\" href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&amp;action=getalbum&amp;album_id=2821072943068839938#wechat_redirect\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><a title=\"\u751f\u4fe1\u5b9e\u64cd\" href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&amp;action=getalbum&amp;album_id=2664545260517294084#wechat_redirect\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a title=\"R\u4ee3\u7801\" href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&amp;action=getalbum&amp;album_id=2812010014583390210#wechat_redirect\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&amp;action=getalbum&amp;album_id=3138206666342268940#wechat_redirect\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<section><img decoding=\"async\" class=\"rich_pages wxw-img\" style=\"text-align: center; font-size: var(--articleFontsize); letter-spacing: 0.034em;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_r0Gd7iaumIGMiaia97aHFV15nrpdzw-173.png?w=640\" data-galleryid=\"\" data-imgfileid=\"100015224\" data-ratio=\"0.2222222222222222\" data-s=\"300,640\" data-type=\"png\" data-w=\"900\" data-recalc-dims=\"1\" \/><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><span style=\"font-size: 16px; font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u5728\u7cbe\u51c6\u533b\u5b66\u7684\u9886\u57df\uff0c\u5982\u4f55\u786e\u5b9a\u836f\u7269\u5f3a\u5927\u7684\u751f\u7269\u6807\u5fd7\u7269\u662f\u7814\u7a76\u4eba\u5458\u4e00\u76f4\u9762\u4e34\u7684\u4e00\u4e2a\u5de8\u5927\u6311\u6218\uff0c\u867d\u7136\u60a3\u8005\u6e90\u6027\u80bf\u7624\u5f02\u79cd\u79fb\u690d(PDX)\u5df2\u7ecf\u662f\u975e\u5e38\u53ef\u9760\u7684\u4e34\u5e8a\u524d\u6a21\u578b\u4e86\uff0c\u4f46\u662f\u7f3a\u4e4f\u8ba1\u7b97\u5de5\u5177\u4f7f\u5f97\u5206\u6790PDX\u7684\u9ad8\u901a\u91cf\u5206\u5b50\u548c\u836f\u7406\u5b66\u7279\u5f81\u53d8\u5f97\u7279\u522b\u56f0\u96be\uff0c\u56e0\u6b64\uff0c\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u7684\u5c31\u662f\u7cbe\u51c6\u533b\u5b66\u5173\u952e\u6311\u6218\u7684\u7834\u5c40\u8005\u2014\u2014Xeva\u3002\u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section style=\"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;\">Xeva (XEnograft Visualization &amp; Analysis)\uff0c\u662f\u4e00\u4e2a\u7528\u4e8e\u4f53\u5185\u836f\u7269\u57fa\u56e0\u7ec4\u5b66\u6570\u636e\u96c6\u7684\u5f00\u6e90\u8f6f\u4ef6\u5305, \u53ef\u4ee5\u91cf\u5316\u57fa\u56e0\u8868\u8fbe\u7684\u53ef\u53d8\u6027\u548c\u8de8PDX\u4f20\u4ee3\u7684\u9014\u5f84\u6d3b\u6027\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/span><\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section style=\"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;\">Xeva\u901a\u8fc7\u4f7f\u7528\u8fc4\u4eca\u4e3a\u6b62\u6700\u5927\u7684PDX\u836f\u7269\u57fa\u56e0\u7ec4\u6570\u636e\u96c6\uff0c\u786e\u5b9a\u4e8687\u79cd\u4e0e51\u79cd\u836f\u7269\u53cd\u5e94\u663e\u8457\u76f8\u5173\u7684\u9014\u5f84(FDR&lt;0.05)\u3002\u53d1\u73b0\u4e86\u57fa\u4e8e\u57fa\u56e0\u8868\u8fbe\u3001\u62f7\u8d1d\u6570\u7578\u53d8\u548c\u7a81\u53d8\u9884\u6d4b\u836f\u7269\u53cd\u5e94\u7684\u65b0\u7684\u751f\u7269\u6807\u5fd7\u7269(\u4e00\u81f4\u6027\u6307\u6570&gt;0.60;FDR&lt; 0.05)\u3002\u603b\u4e4b\uff0cXeva\u4e3a\u4e34\u5e8a\u524d\u4f53\u5185\u836f\u7269\u57fa\u56e0\u7ec4\u5b66\u6570\u636e\u7684\u7efc\u5408\u5206\u6790\u63d0\u4f9b\u4e86\u4e00\u4e2a\u7075\u6d3b\u7684\u5e73\u53f0\uff0c\u4ee5\u8bc6\u522b\u9884\u6d4b\u836f\u7269\u53cd\u5e94\u7684\u751f\u7269\u6807\u5fd7\u7269\uff0c\u4ee3\u8868\u7740\u7cbe\u51c6\u80bf\u7624\u5b66\u7684\u91cd\u8981\u4e00\u6b65\uff01<\/span><span style=\"font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u00a0\u00a0<\/span><\/span><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"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;\">\u4ecb\u7ecd\u4e86\u8fd9\u4e48\u591a\uff0c\u5c0f\u679c\u5df2\u7ecf\u8dc3\u8dc3\u6b32\u8bd5\u5566\uff01\u4eca\u5929\u5c0f\u679c\u5c31\u6765\u624b\u628a\u624b\u6559\u4f1a\u5927\u5bb6\u5982\u4f55\u4f7f\u7528Xeva\u8fd9\u4e2aR\u5305\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #ff0000;\" data-darkreader-inline-color=\"\">\u672c\u6b21\u6559\u7a0b\u5bf9\u7535\u8111\u914d\u7f6e\u6709\u4e00\u5b9a\u9700\u6c42\uff0c\u5efa\u8bae\u5927\u5bb6\u4f7f\u7528\u670d\u52a1\u5668\u8fd0\u884c\uff0c\u5982\u679c\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u6211\u4eec\u6765\u79df\u8d41\u670d\u52a1\u5668\u54e6\uff5e<\/span><span style=\"color: #ff0000; font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\" data-darkreader-inline-color=\"\">\u00a0\u00a0<\/span><\/span><span style=\"color: #ff0000; font-family: \u7b49\u7ebf; letter-spacing: 0.034em; font-size: 16px;\" data-darkreader-inline-color=\"\">\u00a0 \u00a0<\/span><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"font-size: 15px; padding-right: 2px; padding-left: 2px; margin-bottom: 0px;\">\n<section style=\"text-align: center; justify-content: center; display: flex; flex-flow: row; margin-top: 10px; margin-bottom: 10px;\">\n<section style=\"display: inline-block; width: 100%; vertical-align: top; align-self: flex-start; flex: 0 0 auto; height: auto;\">\n<section style=\"display: flex; width: 100%; flex-flow: column;\">\n<section style=\"z-index: 1; transform: perspective(0px); transform-style: flat;\">\n<section style=\"justify-content: center; display: flex; flex-flow: row; transform: translate3d(4px, 0px, 0px) rotateX(180deg); margin-bottom: -2px;\">\n<section style=\"display: inline-block; vertical-align: top; width: 50%; align-self: flex-start; flex: 0 0 auto;\">\n<section>\n<section style=\"display: inline-block; width: 10px; height: 14px; vertical-align: top; overflow: hidden; background-color: #5b5b5b; border: 2px solid #ffffff;\" data-darkreader-inline-bgcolor=\"\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section style=\"text-align: justify;\">\n<p style=\"text-wrap: wrap;\">\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: top; width: 50%;\">\n<section>\n<section style=\"display: inline-block; width: 10px; height: 14px; vertical-align: top; overflow: hidden; background-color: #5b5b5b; border: 2px solid #ffffff;\" data-darkreader-inline-bgcolor=\"\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section style=\"text-align: justify;\">\n<p style=\"text-wrap: wrap;\">\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left; justify-content: flex-start; display: flex; flex-flow: row;\">\n<section style=\"display: inline-block; width: 100%; vertical-align: top; align-self: flex-start; flex: 0 0 auto; background-color: #c2d1ff;\" data-darkreader-inline-bgcolor=\"\">\n<section style=\"text-align: center; justify-content: center; display: flex; flex-flow: row; margin-top: -4px; margin-bottom: 5px; transform: translate3d(5px, 0px, 0px);\">\n<section style=\"display: inline-block; width: 100%; vertical-align: top; align-self: flex-start; flex: 0 0 auto; background-color: #c1d1ff; padding: 10px 20px; box-shadow: #ffffff -2px 2px 0px;\" data-darkreader-inline-bgcolor=\"\" data-darkreader-inline-boxshadow=\"\">\n<section style=\"text-align: left; justify-content: flex-start; display: flex; flex-flow: row;\">\n<section style=\"display: inline-block; vertical-align: middle; align-self: center; flex: 0 0 auto; width: 100%; height: auto;\">\n<section style=\"text-align: center; color: #000000;\" data-darkreader-inline-color=\"\"><strong>\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/strong><\/p>\n<p><strong>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6<\/strong><\/p>\n<p><strong>\u6587\u4ef6\u7f16\u53f7\uff1a240118<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-wrap: wrap;\"><span style=\"color: #ab1942;\" data-darkreader-inline-color=\"\"><strong>\u9700\u8981\u79df\u8d41\u670d\u52a1\u5668\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u626b\u7801\u6dfb\u52a0\u5c0f\u679c\uff0c\u6b64\u5916\u5c0f\u679c\u8fd8\u63d0\u4f9b\u751f\u4fe1\u5206\u6790\uff0c\u601d\u8def\u8bbe\u8ba1\uff0c\u6587\u732e\u590d\u73b0\u7b49\uff0c\u6709\u9700\u8981\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u64a9~<\/strong><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" style=\"width: 170px; height: 170px;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_f6PG40Qrdu5e9B1iaIMItPiajABYWA-67.jpg?w=640\" data-galleryid=\"\" data-imgfileid=\"100015243\" data-ratio=\"1\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"430\" data-recalc-dims=\"1\" \/><span style=\"text-align: justify; font-size: 16px; color: #ff0000; font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\" data-darkreader-inline-color=\"\">\u00a0 \u00a0<\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/p>\n<\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section 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;\">Step 1 \u5b89\u88c5Xeva<\/span><\/section>\n<section style=\"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;\"> \u00a0<\/span><span style=\"letter-spacing: 0.034em; font-family: \u7b49\u7ebf; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal;\">\u5206\u6790\u6240\u9700\u7684\u6570\u636e\u5c0f\u679c\u5df2\u7ecf\u5e2e\u5927\u5bb6\u51c6\u5907\u597d\u4e86~<\/span><span style=\"letter-spacing: 0.034em; font-family: \u7b49\u7ebf;\">\u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/span><\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section 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;\">\u94fe\u63a5\uff1ahttps:\/\/pan.baidu.com\/s\/1E9LxoIqMYYvBJKtkSkGN4A<\/span><\/section>\n<section style=\"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;\">\u63d0\u53d6\u7801\uff1ax54w<\/span><span style=\"letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0<\/span><\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td style=\"border: initial none initial;\" width=\"0.0\" height=\"34.400524\"><\/td>\n<td style=\"border: initial none initial;\" width=\"0.0\" height=\"34.400524\"><\/td>\n<\/tr>\n<tr>\n<td style=\"border: initial none initial;\"><\/td>\n<td style=\"border: initial none initial;\">\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_0KzZictibujT3mppewekyFz3DHamKw.png?resize=377%2C290\" width=\"377 .3399963378906\" height=\"290 .07000732421875\" data-imgfileid=\"100015117\" data-ratio=\"0.7687861271676301\" data-type=\"png\" data-w=\"865\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n<\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"letter-spacing: 0.034em; font-family: \u7b49\u7ebf; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; color: #000000;\" data-darkreader-inline-color=\"\">\u56fe\u4e2d\u7684\u6570\u636e\u662f\u6211\u4eec\u672c\u6b21\u5206\u6790\u6240\u6d89\u53ca\u5230\u7684\u4e00\u4e9b\u836f\u7269\u901a\u8def\uff0c\u4f8b\u5982\u56fe\u4e2d\u7ed9\u51fa\u4e86MAPK\u76f8\u5173\u7684\u4fe1\u53f7\u901a\u8def<\/span><span style=\"letter-spacing: 0.034em; font-family: \u7b49\u7ebf; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-alternates: normal; font-variant-position: normal; color: #0070c0;\" data-darkreader-inline-color=\"\">\u3002<\/span><\/span><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #0070c0; font-size: 16px;\" data-darkreader-inline-color=\"\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/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<li><\/li>\n<\/ul>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u68c0\u67e5\u548c\u5b89\u88c5Xeva<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(devtools)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if(is.element(\"Xeva\", installed.packages())==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;\">  install_github(\"bhklab\/Xeva\")<\/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;\">library(Xeva)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><\/section>\n<\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section 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;\">Step 2 \u5206\u6790\u836f\u7269\u5bf9\u4e8e\u4e73\u817a\u764c\u7684\u6709\u6548\u6027<\/span><\/section>\n<section 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;\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/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<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<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5b89\u88c5\u6240\u9700R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(methods)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(BBmisc)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(Xeva)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u52a0\u8f7d\u60a3\u8005\u7684\u80bf\u7624\u53cd\u5e94\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">data(pdxe)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5c06\u80bf\u7624\u7684\u7f29\u5199\u548c\u5168\u79f0\u5bf9\u5e94\uff0c\u65b9\u4fbf\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tumor &lt;- c(\"BRCA\" = \"Breast Cancer\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"NSCLC\" = \"Non-small Cell Lung Carcinoma\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"PDAC\" = \"Pancreatic Ductal Carcinoma\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"CM\" = \"Cutaneous Melanoma\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"GC\" = \"Gastric Cancer\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"CRC\" = \"Colorectal Cancer\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8f93\u51faPDF\u6587\u4ef6\uff0c\u6839\u636eXeva\u4e2d\u7684mRECIST \u6807\u51c6\uff0c\u6309\u7167\u60a3\u8005\u7684ID\u548c\u80bf\u7624\u7c7b\u578b\u8fdb\u884c\u4e86\u5206\u7ec4\uff0c\u5f97\u5230\u4e86\u4e00\u4e2a\u65b0\u7684\u6570\u636e\u96c6 pdxe.tt<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(\"..\/results\/figure-1.pdf\", width = 14.1, height = 7.6)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for(tt in names(tumor))<\/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;\">  pdxe.tt &lt;- summarizeResponse(pdxe, response.measure = \"mRECIST\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">group.by=\"patient.id\", tissue=tt)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  pdxe.tt &lt;- pdxe.tt[, names(sort(pdxe.tt[\"untreated\", ], na.last = TRUE))]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  plotmRECIST(pdxe.tt, control.name = \"Untreated\", name = tumor[tt],<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">              row_fontsize = 12, col_fontsize=12, sort = 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;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><\/section>\n<\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_rv1Kia9UmPYQuSGQiaX0ibd3G7POTQ.png?resize=553%2C298\" width=\"553 .739990234375\" height=\"298 .3399963378906\" data-imgfileid=\"100015121\" data-ratio=\"0.5388888888888889\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/section>\n<section 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;\">\u901a\u8fc7\u4f7f\u7528Xeva\u7684mRECIST\u51fd\u6570\u8ba1\u7b97\u548c\u53ef\u89c6\u5316PDXE\u4e73\u817a\u764c\u6570\u636e\u4e2d\u57fa\u4e8ePDX\u7684\u836f\u7269\u7b5b\u9009\u7684\u54cd\u5e94\u3002<\/span><\/section>\n<section style=\"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; color: #111111;\" data-darkreader-inline-color=\"\">\u4ece\u56fe\u7247\u4e2d\u53ef\u4ee5\u770b\u5230\uff0c\u6709\u4e9b\u6cbb\u7597\u7684\u6548\u679c\u6bd4\u8f83\u597d\uff0c\u6bd4\u5982\u00a0<\/span><strong style=\"font-weight: bold; mso-bidi-font-weight: bold; mso-bidi-font-size: 10.5pt; font-family: -apple-system; mso-ascii-font-family: -apple-system; mso-fareast-font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">BGJ398<\/strong><span style=\"font-family: -apple-system; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\u00a0\u548c\u00a0<\/span><strong style=\"font-weight: bold; mso-bidi-font-weight: bold; mso-bidi-font-size: 10.5pt; font-family: -apple-system; mso-ascii-font-family: -apple-system; mso-fareast-font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">binimetinib<\/strong><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\uff0c\u6709\u5f88\u591a\u7ea2\u8272\u7684\u683c\u5b50\uff0c\u8868\u793a\u5b8c\u5168\u53cd\u5e94\uff08CR\uff09\u3002\u6709\u4e9b\u6cbb\u7597\u7684\u6548\u679c\u6bd4\u8f83\u5dee\uff0c\u6bd4\u5982\u00a0<\/span><strong style=\"font-weight: bold; mso-bidi-font-weight: bold; mso-bidi-font-size: 10.5pt; font-family: -apple-system; mso-ascii-font-family: -apple-system; mso-fareast-font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">paclitaxel<\/strong><span style=\"font-family: -apple-system; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\u00a0\u548c\u00a0<\/span><strong style=\"font-weight: bold; mso-bidi-font-weight: bold; mso-bidi-font-size: 10.5pt; font-family: -apple-system; mso-ascii-font-family: -apple-system; mso-fareast-font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">LLM871<\/strong><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\uff0c\u5b83\u4eec\u6709\u5f88\u591a\u84dd\u8272\u7684\u683c\u5b50\uff0c\u8868\u793a\u8fdb\u5c55\u6027\u75be\u75c5\uff08PD\uff09\u3002\u6709\u4e9b\u6cbb\u7597\u7684\u6548\u679c\u6bd4\u8f83\u4e00\u822c\uff0c\u6bd4\u5982<\/span><strong style=\"font-weight: bold; mso-bidi-font-weight: bold; mso-bidi-font-size: 10.5pt; font-family: -apple-system; mso-ascii-font-family: -apple-system; mso-fareast-font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">LEE011+everolimus<\/strong><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\uff0c\u6709\u5f88\u591a\u7eff\u8272\u7684\u683c\u5b50\uff0c\u8868\u793a\u7a33\u5b9a\u75c5\u60c5\uff08SD\uff09\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none;\">\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u5206\u6790\u54ea\u4e9b\u836f\u7269\u5bf9\u54ea\u4e9b\u60a3\u8005\u6709\u6548\uff0c\u4ee5\u53ca\u54ea\u4e9b\u836f\u7269\u53ef\u80fd\u6709\u526f\u4f5c\u7528\u6216\u65e0\u6548\u3002<\/span> \u00a0 \u00a0<\/span><\/section>\n<section 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;\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/section>\n<section 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;\">Step 3 \u5bf9\u57fa\u56e0\u6570\u636e\u8fdb\u884cTSNE\u5206\u6790\uff0c\u76f8\u5173\u6027\u5206\u6790<\/span><\/section>\n<section 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;\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/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<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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bfc\u5165\u529f\u80fd\u51fd\u6570\uff0c\u6240\u7528\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">set.seed(19)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8c03\u7528\u529f\u80fd\u51fd\u6570\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">source(\"imp_functions.R\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">suppressMessages(library(Biobase))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(Rtsne)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(ggplot2)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(ggpubr)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u51c6\u5907\u8f93\u51fa\u7ed3\u679c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">args &lt;- commandArgs(trailingOnly = TRUE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">recompute &lt;- FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if(args[1] %in% c(TRUE, FALSE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">{ recompute &lt;- args[1] }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(\"..\/results\/figure-2.pdf\", width = 9.27, height = 6.4)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u4ece\"..\/data\/passage_data.Rda\"\u6587\u4ef6\u4e2d\u8bfb\u53d6\u901a\u9053\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">passage &lt;- readRDS(\"..\/data\/passage_data.Rda\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dp &lt;- pData(passage$data)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bf9\u6570\u636e\u8fdb\u884ct-SNE\uff08t\u5206\u5e03\u968f\u673a\u90bb\u5c45\u5d4c\u5165\uff09\u964d\u7ef4\u5904\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8ba1\u7b97\u80bf\u7624\u5bf9\u5e94\u7684\u60a3\u8005\u6570\u91cf\uff0c\u6392\u5e8f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">ptByTT &lt;- sort(sapply(unique(dp$tumor.type),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">function(tt){length(unique(dp[dp$tumor.type==tt, \"patient.id\"]))},<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">                      USE.NAMES = TRUE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u7b5b\u9009\u6570\u91cf\u5927\u4e8e10\u7684\u80bf\u7624\u7c7b\u578b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tt2take &lt;- names(ptByTT)[ptByTT&gt;10]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq &lt;- dp[dp$tumor.type %in% tt2take, ]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">psgFrq&lt;- table(dq$patient.id)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pid2take &lt;- names(psgFrq)[psgFrq&gt;1]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq &lt;- dq[dq$patient.id%in%pid2take, ]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq$tumor.type &lt;- gsub(\"_\", \" \", dq$tumor.type)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq$tumor.type[dq$tumor.type==\"large intestine\"] &lt;- \"LI\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tissuCol &lt;- c('#1b9e77','#d95f02','#7570b3','#e7298a', '#d9f0a3', '#e6ab02','#a6761d','#666666')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">names(tissuCol) &lt;- c(\"lung\", \"ovary\", \"LI\", \"breast\", \"kidney\", \"pancreas\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"skin\", \"soft tissue\")    <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u7b5b\u9009\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dt &lt;- as.matrix(t(Biobase::exprs(passage$data)))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dt &lt;- dt[dq$biobase.id, ]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8fd0\u884ct-SNE\u7b97\u6cd5\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tsne_out &lt;- Rtsne(dt, perplexity = 13)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq$X &lt;- data.frame(tsne_out$Y)[,1]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dq$Y &lt;- data.frame(tsne_out$Y)[,2]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u8fdb\u884c\u53ef\u89c6\u5316\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tsne.plot &lt;- ggplot(data=dq, aes(X, Y, color=tumor.type)) + geom_point(size=0.5)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tsne.plot &lt;- tsne.plot + theme_classic()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tsne.plot &lt;- tsne.plot + scale_color_manual(values=tissuCol)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tsne.plot &lt;- tsne.plot + geom_line(data=dq, aes(X, Y, group=patient.id),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">                                   show.legend=FALSE)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">print(tsne.plot)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u5bf9\u80bf\u7624\u6570\u636e\u7684\u76f8\u5173\u6027\u8fdb\u884c\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">marExp &lt;- Biobase::exprs(passage$data)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">passMat &lt;- passage$passage<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># \u8fc7\u6ee4\u6709\u591a\u4e2a\u975e NA \u503c\u7684\u884c\u548c\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">passMat &lt;- passMat %&gt;%     <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  filter(rowSums(!is.na(.)) &gt; 1) %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  filter(colSums(!is.na(.)) &gt; 1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if(recompute==TRUE)<\/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;\">  cat(sprintf(\"recomputing values.... it may take long timen\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  dfx &lt;- data.frame()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">##----- correlation for related pairs ------------<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># use map_dfr to loop over the rows and return a data frame<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  dfx &lt;- passMat %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">    map_dfr(~{<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># use combn to get all possible pairs of non-NA values<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      prx &lt;- combn(.x[!is.na(.x)], 2, simplify = F)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># use map_dbl to loop over the pairs and return a numeric vector<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      v &lt;- prx %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">        map_dbl(~cor(marExp[, .x[1]], marExp[, .x[2]], method = \"pearson\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># return a data frame with correlation and type<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      data.frame(Correlation = v, type = \"Related pairs\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">    })<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># \u4f7f\u7528 sample_n \u83b7\u53d6\u884c\u7684\u968f\u673a\u6837\u672c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  randPassMat &lt;- passMat %&gt;%     <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">    sample_n(nrow(passMat))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># \u4f7f\u7528 map_dfr \u904d\u5386\u884c\u5e76\u8fd4\u56de\u6570\u636e\u5e27<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  dfx &lt;- randPassMat %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">    map_dfr(~{<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># use combn to get all possible pairs of non-NA values<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      prx &lt;- combn(.x[!is.na(.x)], 2, simplify = F)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># use keep to filter the pairs that are not in the same row of passMat<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      prx &lt;- prx %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">keep(~!any(passMat[which(passMat == .x[1]), ] == .x[2]))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u4f7f\u7528 map_dbl \u904d\u5386\u8fd9\u4e9b\u5bf9\u5e76\u8fd4\u56de\u4e00\u4e2a\u6570\u503c\u5411\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      v &lt;- prx %&gt;%<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">        map_dbl(~cor(marExp[, .x[1]], marExp[, .x[2]]))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"># return a data frame with correlation and type<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">      data.frame(Correlation = v, type = \"Random pairs\")<\/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;\">} else<\/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;\">  cat(sprintf(\"using pre-computed valuesn\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">  dfx &lt;- readRDS(\"..\/data\/PDX_passage_correlation.Rda\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pltOrd &lt;- c(\"Related pairs\", \"Random pairs\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dfx$type &lt;- factor(as.character(dfx$type), levels = pltOrd)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pltCol &lt;- c('#e41a1c','#377eb8')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">names(pltCol) &lt;- pltOrd<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">#\u521b\u5efa\u5c0f\u63d0\u7434\u56fe\u548c\u6458\u8981\u7edf\u8ba1\u6570\u636e\uff0c\u4ee5\u6bd4\u8f83\u76f8\u5173\u5bf9\u548c\u968f\u673a\u5bf9\u4e4b\u95f4\u7684\u76f8\u5173\u6027<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- ggplot(data=dfx, aes(x=type, y=Correlation, fill=type, color=type))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + geom_violin(trim=T)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + theme_classic()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + scale_fill_manual(values=pltCol)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + scale_color_manual(values=pltCol)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + stat_summary(fun.data=data_summary, colour = \"white\", size=0.4)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + theme(legend.position=\"none\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + scale_y_continuous(breaks = seq(-1,1,by = 0.1))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + theme(axis.text.x = element_text(colour=\"grey20\",size=12, angle=0,face=\"bold\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">               axis.text.y = element_text(colour=\"grey20\",size=11, face=\"bold\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">               axis.title.y = element_text(colour=\"grey20\",size=11, face=\"bold\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">               axis.ticks.length=unit(0.25,\"cm\"))    <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + theme(axis.line.x = element_line(size = 0, colour = \"white\"),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">               axis.title.x=element_blank(),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">               axis.ticks.x=element_blank())<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">comparisons &lt;- list(c(\"Related pairs\", \"Random pairs\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">p &lt;- p + stat_compare_means(comparisons = comparisons, label = \"p.signif\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">print(p)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">dev.off()<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/>\n<\/span><\/code><\/section>\n<\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td style=\"border: initial none initial;\" width=\"-90.00137\" height=\"10.666828\"><\/td>\n<td style=\"border: initial none initial;\" width=\"-90.00137\" height=\"10.666828\"><\/td>\n<\/tr>\n<tr>\n<td style=\"border: initial none initial;\"><\/td>\n<td style=\"border: initial none initial;\">\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_v56gdDJntRy1qFb2pzAjiavAwEAYoQ.png?resize=640%2C218\" width=\"640 .0780029296875\" height=\"218 .27069091796875\" data-imgfileid=\"100015118\" data-ratio=\"0.34120734908136485\" data-type=\"png\" data-w=\"762\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n<\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"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;\">\u7ed3\u679c\u5982\u56fe\uff0c\u5de6\u56fe\u662f\u5bf9PDXs\u4e0d\u540c\u4f20\u4ee317304\u4e2a\u57fa\u56e0\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884cTSNE\u5206\u6790\uff0c\u4ece\u800c\u5c06\u9ad8\u7ef4\u6570\u636e\u6620\u5c04\u5230\u4f4e\u7ef4\u7a7a\u95f4\uff0c<\/span><span style=\"font-family: \u7b49\u7ebf; font-variant: normal; text-transform: none; color: #111111;\" data-darkreader-inline-color=\"\">\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u80bf\u7624\u5728\u4e8c\u7ef4\u7a7a\u95f4\u4e2d\u7684\u5206\u5e03\u3002\u6bcf\u79cd\u989c\u8272\u4ee3\u8868\u4e00\u79cd\u7279\u5b9a\u7c7b\u578b\u7684\u80bf\u7624\uff0c\u6bd4\u5982\u8bf4\u4e73\u817a\u764c\uff08\u7d2b\u8272\uff09\u7684\u6570\u636e\u70b9\u5206\u5e03\u5f97\u6bd4\u8f83\u5e7f\u6cdb\uff0c\u6709\u4e9b\u70b9\u4e0e\u5176\u4ed6\u7c7b\u578b\u7684\u80bf\u7624\u6df7\u5408\u5728\u4e00\u8d77\uff0c\u6709\u4e9b\u70b9\u5219\u5f62\u6210\u4e86\u4e00\u4e9b\u7c07\u3002\u8fd9\u53ef\u80fd\u8868\u660e\u4e73\u817a\u764c\u7684\u5f02\u8d28\u6027\u6bd4\u8f83\u9ad8\uff0c\u6709\u4e9b\u4e9a\u578b\u4e0e\u5176\u4ed6\u7c7b\u578b\u7684\u80bf\u7624\u66f4\u76f8\u4f3c\uff0c\u6709\u4e9b\u4e9a\u578b\u5219\u66f4\u72ec\u7279\u3002<\/span><\/span><\/section>\n<section style=\"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;\">\u800c\u53f3\u56fe\u662f\u76f8\u5173\u6837\u672c\u5bf9(\u5c5e\u4e8e\u540c\u4e00\u8c31\u7cfb)\u548c\u968f\u673a\u9009\u62e9\u6837\u672c\u5bf9\u7684Pearson\u76f8\u5173\u6027\u7684\u53ef\u89c6\u5316\uff0c\u4ece\u8fd9\u5e45\u56fe\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff1a\u76f8\u5173\u5bf9\u7684\u76f8\u5173\u6027\u7684\u5e73\u5747\u503c\u662f0.94\uff0c\u968f\u673a\u5bf9\u7684\u76f8\u5173\u6027\u7684\u5e73\u5747\u503c\u662f0.86\uff0c\u8bf4\u660e\u4e24\u8005\u4e4b\u95f4\u6709\u663e\u8457\u7684\u5dee\u5f02\u3002<\/span> \u00a0 \u00a0<\/span><\/section>\n<section 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;\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/section>\n<section 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;\">Step 4 \u6240\u6709\u57fa\u56e0\u5728PDX\u4f20\u4ee3\u4e2d\u7684\u7c7b\u5185\u76f8\u5173\u6027(ICC)\u53ef\u89c6\u5316<\/span><\/section>\n<section 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;\"> \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/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=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bfc\u5165\u5305source(\"imp_functions.R\")library(foreach)library(doParallel)library(psych)##plotViolin\uff1a\u4f7f\u7528ggplot2\u5305\u751f\u6210\u5c0f\u63d0\u7434\u56fe\u3002plotViolin &lt;- function(dfx, pltCol, ylim=NULL){  p &lt;- ggplot(data=dfx, aes(x=type, y=ICC , fill=type,color=type))  p &lt;- p + geom_boxplot(width = .001, outlier.size = 2.0, outlier.color = \"#525252\",                        outlier.shape = 95)  p &lt;- p + geom_violin(trim=F)  p &lt;- p + theme_classic()  p &lt;- p + scale_fill_manual(values=pltCol)  p &lt;- p + scale_color_manual(values=pltCol)      p &lt;- p + stat_summary(fun.data=data_summary, colour = \"white\", size=0.4)  p &lt;- p + theme(legend.position=\"none\")  p &lt;- p + scale_y_continuous(breaks = seq(-1,1,by = 0.25))  p &lt;- p + theme(axis.text.x = element_text(colour=\"grey20\",size=12, angle=0,face=\"bold\"),                 axis.text.y = element_text(colour=\"grey20\",size=11, face=\"bold\"),                 axis.title.y = element_text(colour=\"grey20\",size=11, face=\"bold\"),                 axis.ticks.length=unit(0.25,\"cm\"))  p &lt;- p + theme(axis.line.x = element_line(size = 0, colour = \"white\"),                 axis.title.x=element_blank(),                 axis.ticks.x=element_blank())if(!is.null(ylim))  { p &lt;- p + coord_cartesian(ylim = ylim, expand = F) }return(p)}##computeRankMatFor1Gene\u51fd\u6570\uff1a\u8ba1\u7b97\u7ed9\u5b9a\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u7684\u6392\u540d\u77e9\u9635    computeRankMatFor1Gene &lt;- function(gn, pt, marExp){  findRankOfGene &lt;- function(gn, sampleIds, marExp)  {    rtx &lt;- rep(NA, length(sampleIds)); names(rtx)&lt;- names(sampleIds)for(n in names(rtx))    {s &lt;- sampleIds[n]if(!is.na(s))      {        gval &lt;- sort(marExp[, s])        rtx[n] &lt;- which(names(gval)==gn)      }    }return(rtx)  }  gnRankMat &lt;- matrix(data = NA, nrow = nrow(pt), ncol = ncol(pt))  rownames(gnRankMat) &lt;- rownames(pt); colnames(gnRankMat)&lt;- colnames(pt)for(patientID in rownames(pt))  {        sampleIds &lt;- pt[patientID, ]    gnRankMat[patientID, ] &lt;- findRankOfGene(gn, sampleIds, marExp)  }  gnRankMat &lt;- gnRankMat[!apply(gnRankMat, 1, function(x)all(is.na(x))), ]return(gnRankMat)}##getICCforAllGen\u51fd\u6570\uff1a\u7528\u4e8e\u8ba1\u7b97\u6240\u6709\u57fa\u56e0\u7684ICC\uff08Intraclass Correlation Coefficient\uff09\u3002getICCforAllGenes &lt;- function(pt, allGenes, marExp, NCPU=2, verbose=F){if(verbose==TRUE) { cl&lt;-makeCluster(NCPU, outfile=\"\") } else  { cl&lt;-makeCluster(NCPU)}  registerDoParallel(cl)  allICC &lt;- foreach(i=1:length(allGenes), .export=c(\"computeRankMatFor1Gene\"),                    .packages = c(\"psych\") ) %dopar%                    {                      gn &lt;- allGenes[i]                      gnRankMat &lt;- computeRankMatFor1Gene(gn, pt, marExp)                          v &lt;- NULLif(nrow(gnRankMat)&gt;2)                      {                         v &lt;- psych::ICC(gnRankMat, missing = F)                        v$geneName &lt;- gn                      }                      v                    }  stopCluster(cl)  rtx &lt;- data.frame()for(i in 1:length(allICC))  {if(!is.null(allICC[[i]]))    {      v &lt;- allICC[[i]]$results[\"Single_raters_absolute\",]      v[\"gene\"] &lt;- allICC[[i]]$geneName      rtx &lt;- rbind(rtx, v[c(\"ICC\", \"p\", \"gene\")])    }  }  rownames(rtx) &lt;- NULLreturn(rtx)    }## randomizeMatGetICC\u51fd\u6570\uff1a\u7528\u4e8e\u5bf9\u6570\u636e\u8fdb\u884c\u968f\u673a\u5316\u5904\u7406\uff0c\u5e76\u8ba1\u7b97\u968f\u673a\u5316\u540e\u7684\u57fa\u56e0ICC\u503c\u3002randomizeMatGetICC &lt;- function(passMatx, allGenes, marExp, NCPU, verbose=F){  passMatRand &lt;- passMatxfor(i in 1:ncol(passMatRand))  { passMatRand[,i] &lt;- sample(passMatRand[,i]) }for(i in 1:nrow(passMatRand))  { passMatRand[i,] &lt;- sample(passMatRand[i,]) }  passMatRand &lt;- passMatRand[!(apply(passMatRand, 1, function(x) all(is.na(x)))),]  rownames(passMatRand) &lt;- paste0(\"r\", 1:nrow(passMatRand))  allICCRand &lt;- getICCforAllGenes(passMatRand, allGenes, marExp, NCPU=NCPU,                                  verbose=verbose)return(allICCRand)}## \u6570\u636e\u52a0\u8f7d\u548c\u51c6\u5907NCPU = max(1, detectCores()-1 )cat(sprintf(\"n##---- number of CPU %d ------n\", NCPU))passage &lt;- readRDS(\"..\/data\/passage_data.Rda\")dp &lt;- pData(passage$data)mar &lt;- passage$dataallGenes &lt;- rownames(mar)marExp &lt;- Biobase::exprs(mar)pheno &lt;- Biobase::pData(mar)pheno$passage &lt;- paste0(\"P\", pheno$passage)passMat &lt;- passage$passageif(recompute==TRUE){  cat(sprintf(\"recomputing values.... it may take long timen\"))  ICCv &lt;- list()##-------------------------------------------------------##------------------For all tissue type -----------------##-------------------------------------------------------  allICC &lt;- getICCforAllGenes(passMat, allGenes, marExp, NCPU=NCPU, verbose=F)  allICC$type &lt;- \"All tissue\"  allICCRand &lt;- randomizeMatGetICC(passMat, allGenes, marExp, NCPU=NCPU, verbose=F)  allICCRand$type &lt;- \"Null (All tissue)\"  ICCv[[\"All tissue\"]] &lt;- rbind(allICC, allICCRand)##-------------------------------------------------------##------------------By Tissue Type ----------------------  tissueName &lt;- c(\"breast\", \"lung\",  \"pancreas\", \"skin\", \"large_intestine\")for(tt in tissueName)  {      ptt &lt;- passMat[pheno[pheno$tumor.type==tt, \"patient.id\"], , drop=F]if(nrow(ptt)&gt;8)      {        cat(sprintf(\"##--- running for %s -----n\", tt))        allICCtt &lt;- getICCforAllGenes(ptt, allGenes, marExp, NCPU=NCPU, verbose=F)        allICCtt$type &lt;- tt        allICCttRand &lt;- randomizeMatGetICC(ptt,allGenes,marExp,NCPU=NCPU,verbose=F)            allICCttRand$type &lt;- sprintf(\"Null (%s)\", tt)        ICCv[[tt]] &lt;- rbind(allICCtt, allICCttRand)      }##\u50a8\u5b58\u7ed3\u679c  saveRDS(ICCv, \"..\/results\/ICC_for_genes.Rda\")  }} else  {ICCv &lt;- readRDS(\"..\/data\/ICC_for_genes.Rda\")}##\u7ed8\u5236\u56fe\u7247pltColo &lt;- c('#e41a1c', '#8dd3c7','#bebada','#fb8072','#80b1d3','#fdb462')names(pltColo)&lt;-c(\"All tissue\",\"breast\",\"lung\",\"pancreas\",\"skin\",\"large_intestine\")nullCol &lt;- \"#4d4d4d\"pdf(\"..\/results\/figure-3.pdf\", width = 5.15, height = 2.15)for(tt in names(pltColo)){      dfx &lt;- ICCv[[tt]]  pltCol &lt;- c(pltColo[tt], nullCol); names(pltCol) &lt;- c(tt, sprintf(\"Null (%s)\", tt))  dfx$type &lt;- factor(as.character(dfx$type), levels = names(pltCol))  ylim &lt;- c(-0.25,1)  p &lt;- plotViolin(dfx, pltCol, ylim = ylim)print(p)}dev.off()<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td style=\"border: initial none initial;\" width=\"-91.334724\" height=\"32.00049\"><\/td>\n<td style=\"border: initial none initial;\" width=\"-91.334724\" height=\"32.00049\"><\/td>\n<\/tr>\n<tr>\n<td style=\"border: initial none initial;\"><\/td>\n<td style=\"border: initial none initial;\">\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_ryTbYFInQoKYpQO5rofXyDgY25bD9A.png?resize=640%2C132\" width=\"640 .54541015625\" height=\"132 .47341918945312\" data-imgfileid=\"100015119\" data-ratio=\"0.2070365358592693\" data-type=\"png\" data-w=\"739\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n<\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><span style=\"font-size: 16px;\">\u00a0 \u00a0\u00a0<span style=\"letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0<\/span><\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td style=\"border: initial none initial;\" width=\"-90.668045\" height=\"5.3334146\"><\/td>\n<td style=\"border: initial none initial;\" width=\"-90.668045\" height=\"5.3334146\"><\/td>\n<\/tr>\n<tr>\n<td style=\"border: initial none initial;\"><\/td>\n<td style=\"border: initial none initial;\">\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_UWQCUllGNUlRYRRorAv8iaPEtawmWg.png?resize=640%2C277\" width=\"640 .815673828125\" height=\"277 .13818359375\" data-imgfileid=\"100015120\" data-ratio=\"0.43315508021390375\" data-type=\"png\" data-w=\"748\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n<\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<section style=\"margin-top: 8px; margin-bottom: 0px; line-height: 1.6em;\"><\/section>\n<section style=\"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;\">\u5982\u56fe\uff0c\u5c0f\u63d0\u7434\u56fe\u663e\u793a\u4e86\u6240\u6709\u6837\u672c\u7684\u57fa\u56e0\u5728PDX\u4f20\u4ee3\u4e2d\u7684\u7c7b\u5185\u76f8\u5173\u6027(ICC)\uff0c\u5e76\u6309\u7ec4\u7ec7\u7c7b\u578b\u5206\u5c42\u3002\u9ed1\u8272\u7684\u5c0f\u63d0\u7434\u56fe\u8868\u793a\u4f7f\u7528\u975e\u4f20\u4ee3\u76f8\u5173(\u968f\u673a\u9009\u62e9)\u6837\u672c\u8ba1\u7b97\u7684\u57fa\u56e0\u7684ICC\u503c\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section style=\"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;\">\u5c0f\u679c\u4ee5\u7b2c\u4e00\u5e45\u56fe\u4e3a\u4f8b\u5b50\u8fdb\u884c\u8bf4\u660e\uff0c\u8fd9\u5e45\u56fe\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u80bf\u7624\u5728\u901a\u9053\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u3002\u6bcf\u79cd\u989c\u8272\u4ee3\u8868\u4e00\u79cd\u7279\u5b9a\u7c7b\u578b\u7684\u80bf\u7624\u3002\u76f8\u5173\u5bf9\u7684\u76f8\u5173\u6027\u7684\u5e73\u5747\u503c\u662f0.94\uff0c\u968f\u673a\u5bf9\u7684\u76f8\u5173\u6027\u7684\u5e73\u5747\u503c\u662f0.86\uff0c\u4e24\u8005\u4e4b\u95f4\u6709\u663e\u8457\u7684\u5dee\u5f02\uff0c\u8fd9\u4e9b\u56fe\u7247\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u80bf\u7624\u7684\u53ef\u5851\u6027\u548c\u9002\u5e94\u6027\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/span><\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section style=\"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;\">\u4ee5\u4e0a\u5c31\u662f\u5c0f\u679c\u4eca\u5929\u5206\u4eab\u7684\u5168\u90e8\u5185\u5bb9\u5566\uff0c\u5728\u4eca\u5929\u7684\u4ecb\u7ecd\u4e2d\uff0c\u6211\u4eec\u901a\u8fc7\u4f7f\u7528Xeva\u5305\uff0c\u5bf9PDXE\u4e73\u817a\u764c\u4ee5\u53ca\u4e2d\u57fa\u4e8ePDX\u7684\u836f\u7269\u8fdb\u884c\u4e86\u54cd\u5e94\u9776\u5411\u901a\u8def\u7684\u7b5b\u9009\uff0c\u5e76\u4e14\u4f7f\u7528t-SNE\u5bf9\u4e73\u817a\u764c\u76f8\u5173\u7684\u6570\u636e\u8fdb\u884c\u4e86\u964d\u7ef4\u5904\u7406\uff0c\u6700\u540e\u901a\u8fc7\u5206\u6790\u8bf4\u660ePDX\u6a21\u578b\u80fd\u591f\u4fdd\u6301\u539f\u59cb\u80bf\u7624\u7684\u57fa\u56e0\u8868\u8fbe\u7684\u7a33\u5b9a\u6027\u548c\u4e00\u81f4\u6027\uff0c\u8fdb\u800c\u4e3a\u7cbe\u51c6\u533b\u5b66\u7684\u63a2\u7d22\u63d0\u4f9b\u4e86\u826f\u597d\u7684\u4fdd\u969c\u3002<\/span><span style=\"font-family: \u7b49\u7ebf; letter-spacing: 0.034em;\">\u00a0 \u00a0 \u00a0 \u00a0\u00a0<\/span><\/span><span style=\"font-size: 16px;\">\u00a0<\/span><\/section>\n<section style=\"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; color: #ff0000;\" data-darkreader-inline-color=\"\">\u9664\u4e86\u4eca\u5929\u5c0f\u679c\u4ecb\u7ecd\u7684\u529f\u80fd\u4e4b\u5916\uff0cXeva\u5305\u4e2d\u8fd8\u6709\u5f88\u591a\u7684\u529f\u80fd\u7b49\u7740\u5c0f\u4f19\u4f34\u4eec\u53bb\u63a2\u7d22\uff0c\u5982\u679c\u6709\u5176\u4ed6\u751f\u4fe1\u65b9\u5411\u7684\u4efb\u4f55\u7591\u95ee\uff0c\u6b22\u8fce\u5927\u5bb6\u5173\u6ce8\u5c0f\u679c\uff0c\u8bd5\u4e00\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\uff0c\u5c31\u53ef\u4ee5\u76f4\u63a5\u7ed8\u5236\u60f3\u8981\u7684\u56fe\u5462\uff0c\u94fe\u63a5\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span>\u00a0 \u00a0\u00a0<\/span><\/section>\n<section style=\"margin-bottom: 0px;\">\n<section>\n<section>\n<section>\n<section>\n<section>\n<section>\n<section>\n<section>\n<p style=\"text-indent: 0px; margin-bottom: 0px;\"><span style=\"color: #007aaa;\" data-darkreader-inline-color=\"\"><strong><span style=\"color: #007aaa; letter-spacing: 0.578px; text-indent: 32px; text-wrap: wrap; background-color: #ffffff; font-size: 15px;\" data-darkreader-inline-color=\"\" data-darkreader-inline-bgcolor=\"\">\u5c0f\u679c\u8fd8<span style=\"color: #007aaa; background-color: #ffffff; font-size: 15px; letter-spacing: 0.578px; text-decoration: none solid rgba(0, 0, 0, 0.9);\" data-darkreader-inline-color=\"\" data-darkreader-inline-bgcolor=\"\">\u63d0\u4f9b\u601d\u8def\u8bbe\u8ba1\u3001\u5b9a\u5236\u751f\u4fe1\u5206\u6790\u3001\u6587\u732e\u601d\u8def\u590d\u73b0\uff1b\u6709\u9700\u8981\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u76f4\u63a5\u626b\u7801\u54a8\u8be2\u5c0f\u679c\uff0c\u7aed\u8bda\u4e3a\u60a8\u7684\u79d1\u7814\u52a9\u529b\uff01<\/span><\/span><\/strong><\/span><\/p>\n<p style=\"margin-bottom: 0px;\">\n<section style=\"font-size: 15px; padding-right: 2px; padding-left: 2px; margin-bottom: 0px;\">\n<section style=\"text-align: center; justify-content: center; display: flex; flex-flow: row;\">\n<section style=\"display: inline-block; width: 100%; vertical-align: top; flex: 0 0 auto; height: auto; box-shadow: #c2d1ff -5px 5px 0px; align-self: flex-start; border: 1px solid #727272;\" data-darkreader-inline-boxshadow=\"\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section style=\"justify-content: center; display: flex; flex-flow: row;\">\n<section style=\"display: inline-block; width: 42.6829%; vertical-align: middle; box-shadow: #2b416e 0px 0px 0px; flex: 0 0 auto; height: auto; padding-left: 10px; align-self: center;\" data-darkreader-inline-boxshadow=\"\">\n<section style=\"margin-top: 10px; margin-bottom: 10px; line-height: 0; transform: translate3d(20px, 0px, 0px);\">\n<section style=\"vertical-align: middle; display: inline-block; line-height: 0; width: 75%; height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" style=\"vertical-align: middle; width: 100%;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_B2jkicacLzPjw4xMSqVvoucZjonVDA-5.jpg?w=640\" data-imgfileid=\"100015237\" data-ratio=\"1\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"430\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: middle; width: 56.9106%; flex: 0 0 auto; height: auto; align-self: center;\">\n<section style=\"line-height: 2; letter-spacing: 1px; color: #2b416e;\" data-darkreader-inline-color=\"\">\n<p style=\"margin-bottom: 2px;\"><strong>\u5b9a\u5236\u751f\u4fe1\u5206\u6790<\/strong><\/p>\n<p style=\"margin-bottom: 2px;\"><strong>\u670d\u52a1\u5668\u79df\u8d41<\/strong><\/p>\n<p><strong>\u626b\u7801\u54a8\u8be2\u5c0f\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-wrap: wrap;\">\n<section style=\"text-align: center; margin-top: 10px; margin-bottom: 10px; line-height: 0;\">\n<section style=\"vertical-align: middle; display: inline-block; line-height: 0;\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247497780&amp;idx=2&amp;sn=7eee90af6f387e4153bba13028e545a1&amp;chksm=cf7f68f1f808e1e7dfb3a0597ef442e5c6e700ecf6ee5a035c766a4c7486c12eabd0ab218ea6&amp;scene=21#wechat_redirect\" target=\"_blank\" rel=\"noopener\" data-itemshowtype=\"0\" data-linktype=\"1\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" style=\"vertical-align: middle; width: 100%;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_7TvAyUibd1TPhJmZfialJtv6tu2SEg-5.png?w=640\" data-imgfileid=\"100015238\" data-ratio=\"0.3253333333333333\" data-s=\"300,640\" data-type=\"png\" data-w=\"750\" data-recalc-dims=\"1\" \/><\/span><\/a><\/section>\n<\/section>\n<section style=\"text-align: center; margin-top: 10px; margin-bottom: 10px; line-height: 0;\">\n<section style=\"vertical-align: middle; display: inline-block; line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img js_insertlocalimg\" style=\"letter-spacing: 0.578px; text-align: center; text-wrap: wrap;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_9N02aBaau07RufXeXRLmvAHsrFZxtw-5.jpg?w=640\" data-imgfileid=\"100015239\" data-ratio=\"0.3811111111111111\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"900\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"display: flex; flex-flow: row; margin-top: 10px; margin-right: 0%; margin-left: 0%; text-align: left; justify-content: flex-start;\">\n<section style=\"display: inline-block; vertical-align: bottom; width: auto; min-width: 10%; flex: 0 0 auto; height: auto; align-self: flex-end; padding-right: 2px; padding-left: 2px;\">\n<section style=\"margin: 10px 0% 2px; transform: translate3d(2px, 0px, 0px);\">\n<section style=\"font-size: 16px; color: #3a425e; line-height: 1; letter-spacing: 5px; text-align: center;\" data-darkreader-inline-color=\"\"><strong>\u5f80\u671f\u56de\u987e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-right: 0%; margin-left: 0%;\">\n<section style=\"height: 3px; background-color: #5f9cef;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<section style=\"margin-top: 2px; margin-right: 0%; margin-left: 0%; text-align: center; line-height: 0.8; font-size: 9px;\">\n<section style=\"width: 0px; display: inline-block; border-top: 0.8em solid #3a425e; border-left: 0.7em solid transparent !important; border-right: 0.7em solid transparent !important;\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-left=\"\" data-darkreader-inline-border-right=\"\"><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: bottom; width: auto; flex: 100 100 0%; align-self: flex-end; height: auto;\">\n<section style=\"margin-right: 0%; margin-left: 0%;\">\n<section style=\"height: 3px; background-color: #5f9cef;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<section style=\"margin-top: 2px; margin-right: 0%; margin-left: 0%; text-align: center; line-height: 0.8; font-size: 9px;\">\n<section style=\"width: 0px; display: inline-block; border-top: 0.8em solid rgba(255, 255, 255, 0); border-left: 0.7em solid transparent !important; border-right: 0.7em solid transparent !important;\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-left=\"\" data-darkreader-inline-border-right=\"\"><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"min-height: 40px; margin: 10px 0%;\">\n<section style=\"width: 100%; margin-right: auto; margin-bottom: -10px; margin-left: auto;\">\n<table width=\"100%\">\n<tbody>\n<tr>\n<td style=\"border-color: #3e3e3e; border-style: none; padding: 0px;\" colspan=\"1\" rowspan=\"1\" width=\"100.0000%\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section>\n<section style=\"display: flex; flex-flow: row; margin-top: 10px; margin-right: 0%; margin-left: 0%; justify-content: flex-start;\">\n<section style=\"display: inline-block; vertical-align: middle; width: auto; min-width: 10%; height: auto; flex: 0 0 auto; align-self: center; box-shadow: #000000 0px 0px 0px;\" data-darkreader-inline-boxshadow=\"\">\n<section style=\"font-size: 19px; color: #5f9cef; line-height: 1;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><strong>01<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: middle; width: auto; flex: 100 100 0%; align-self: center; height: auto;\">\n<section style=\"color: #8c8c8c;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><span style=\"color: #e0e0e0;\" data-darkreader-inline-color=\"\">\uff5c<a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247497780&amp;idx=2&amp;sn=7eee90af6f387e4153bba13028e545a1&amp;chksm=cf7f68f1f808e1e7dfb3a0597ef442e5c6e700ecf6ee5a035c766a4c7486c12eabd0ab218ea6&amp;scene=21#wechat_redirect\" target=\"_blank\" rel=\"noopener\" data-itemshowtype=\"0\" data-linktype=\"2\">1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff0c\u4e24\u4eba\u6210\u56e2\uff0c1\u4eba\u514d\u5355\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\">\n<section style=\"background-color: #e0e0e0; height: 1px;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr>\n<td style=\"border-color: #3e3e3e; border-style: none; padding: 0px;\" colspan=\"1\" rowspan=\"1\" width=\"100.0000%\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section>\n<section style=\"display: flex; flex-flow: row; margin-top: 10px; margin-right: 0%; margin-left: 0%; justify-content: flex-start;\">\n<section style=\"display: inline-block; vertical-align: middle; width: auto; min-width: 10%; height: auto; flex: 0 0 auto; align-self: center;\">\n<section style=\"font-size: 19px; color: #5f9cef; line-height: 1;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><strong>02<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: middle; width: auto; flex: 100 100 0%; align-self: center; height: auto;\">\n<section style=\"color: #8c8c8c;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><span style=\"color: #e0e0e0;\" data-darkreader-inline-color=\"\">\uff5c<a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247498878&amp;idx=1&amp;sn=fc34ed3f1d15d060bbaf8166adcebd58&amp;chksm=cf7f6cbbf808e5ad0b5417e50ed75cfbd1b3a83ac43b97f1dfa718c822878a9a004990075133&amp;scene=21#wechat_redirect\" target=\"_blank\" rel=\"noopener\" data-itemshowtype=\"0\" data-linktype=\"2\">\u5355\u4e2a\u6570\u636e\u5e93\u7528\u817b\u4e86\uff1f\u591a\u6570\u636e\u5e93\u201c\u7ec4\u5408\u62f3\u201d\u5e26\u4f60\u6253\u5f00\u514d\u75ab\u6d78\u6da6\u65b0\u601d\u8def\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\">\n<section style=\"background-color: #e0e0e0; height: 1px;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr>\n<td style=\"border-color: #3e3e3e; border-style: none; padding: 0px;\" colspan=\"1\" rowspan=\"1\" width=\"100.0000%\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section>\n<section style=\"display: flex; flex-flow: row; margin-top: 10px; margin-right: 0%; margin-left: 0%; justify-content: flex-start;\">\n<section style=\"display: inline-block; vertical-align: middle; width: auto; min-width: 10%; height: auto; flex: 0 0 auto; align-self: center;\">\n<section style=\"font-size: 19px; color: #5f9cef; line-height: 1;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><strong>03<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: middle; width: auto; flex: 100 100 0%; align-self: center; height: auto;\">\n<section style=\"color: #8c8c8c;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><span style=\"color: #e0e0e0;\" data-darkreader-inline-color=\"\">\uff5c<a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247498673&amp;idx=1&amp;sn=1e09b74a836c1e64a62ae1f66eeb3f93&amp;chksm=cf7f6b74f808e262de70be43fd73bf5fefdc0914e525eb2032f741a0152e619689cedc76946f&amp;scene=21#wechat_redirect\" target=\"_blank\" rel=\"noopener\" data-itemshowtype=\"11\" data-linktype=\"2\">\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7684\u51c6\u5907\u5de5\u4f5c\uff0cGWAS\u6570\u636e\u7684\u7f51\u7ad9\u4e0b\u8f7d\u65b9\u6cd5<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\">\n<section style=\"background-color: #e0e0e0; height: 1px;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr>\n<td style=\"border-color: #3e3e3e; border-style: none; padding: 0px;\" colspan=\"1\" rowspan=\"1\" width=\"100.0000%\" data-darkreader-inline-border-top=\"\" data-darkreader-inline-border-right=\"\" data-darkreader-inline-border-bottom=\"\" data-darkreader-inline-border-left=\"\">\n<section>\n<section style=\"display: flex; flex-flow: row; margin-top: 10px; margin-right: 0%; margin-left: 0%; justify-content: flex-start;\">\n<section style=\"display: inline-block; vertical-align: middle; width: auto; min-width: 10%; height: auto; flex: 0 0 auto; align-self: center;\">\n<section style=\"font-size: 19px; color: #5f9cef; line-height: 1;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><strong>04<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block; vertical-align: middle; width: auto; flex: 100 100 0%; align-self: center; height: auto;\">\n<section style=\"color: #8c8c8c;\" data-darkreader-inline-color=\"\">\n<p style=\"text-wrap: wrap;\"><span style=\"color: #e0e0e0;\" data-darkreader-inline-color=\"\">\uff5c<a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&amp;mid=2247498517&amp;idx=1&amp;sn=fa3c0104cee316982fe8162b79fe234f&amp;chksm=cf7f6bd0f808e2c6cf979704bf883cfb5480444604f90da61dc286e7541fa5bb49df0a2fb58a&amp;scene=21#wechat_redirect\" target=\"_blank\" rel=\"noopener\" data-itemshowtype=\"0\" data-linktype=\"2\">\u8ddf\u7740\u5c0f\u679c\u5b66\u590d\u73b0-\u624b\u628a\u624b\u5e26\u4f60\u62ff\u4e0bIF=46.9Nature \u7ea7\u522b\u7684\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u56fe\uff01\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\">\n<section style=\"background-color: #e0e0e0; height: 1px;\" data-darkreader-inline-bgcolor=\"\"><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\">\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>\u600e\u6837\u8fc8\u51fa\u7cbe\u51c6\u533b\u5b66\u5206\u6790\u7b2c\u4e00\u6b65\uff1fXeva\u5e2e\u4f60\u6253\u597d\u836f\u7269\u9776\u5411\u7684\u57fa\u7840\uff01 \u539f\u521b\u00a0\u00a0\u5c0f\u679c\u00a0\u00a0\u751f\u4fe1\u679c\u00a0\u00a02024-01-18  [&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\/58492"}],"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=58492"}],"version-history":[{"count":2,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58492\/revisions"}],"predecessor-version":[{"id":58504,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58492\/revisions\/58504"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58492"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58492"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58492"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}