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 <o:p> <\/o:p><\/span><\/section>\n<section style=\"text-align: justify;margin-left: 0pt;font-size: 10.5pt;font-family: \u7b49\u7ebf;font-weight: normal;text-indent: 0pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 16px;\">\u9996\u5148\uff0c\u5c0f\u679c\u5e2e\u5927\u5bb6\u7406\u6e05\u5bf9\u80bf\u7624\u8fdb\u884c\u521d\u6b65\u5206\u6790\u7684\u601d\u8def\uff0c\u5728\u83b7\u53d6\u80bf\u7624\u7684\u76f8\u5173\u6570\u636e\u540e\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u6574\u5408\u5206\u6790\uff0c\u8bc4\u4f30\u7279\u5b9a\u7ec4\u7ec7\u533a\u57df\u4e2d\u7279\u5b9a\u7ec6\u80de\u7c7b\u578b\u7684\u5bcc\u96c6\u7a0b\u5ea6\uff0c\u7136\u540e\u518d\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u3002<\/span><\/section>\n<section style=\"text-align: justify;margin-left: 0pt;font-size: 10.5pt;font-family: \u7b49\u7ebf;font-weight: normal;text-indent: 0pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 16px;\">          <o:p> <\/o:p><\/span><\/section>\n<section style=\"text-align: justify;margin-left: 0pt;font-size: 10.5pt;font-family: \u7b49\u7ebf;font-weight: normal;text-indent: 0pt;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 16px;\">\u6211\u4eec\u5728\u53cd\u6620\u57fa\u56e0\u7684\u5dee\u5f02\u8868\u8fbe\u7a0b\u5ea6\u65f6\uff0c\u901a\u5e38\u4f7f\u7528\u7684\u662f\u5e73\u5747\u5bf9\u6570\u6298\u53e0\u53d8\u5316\uff08avg_logFC\uff09\u3002avg_logFC\u6307\u7684\u662f\u4e24\u7ec4\u6837\u672c\uff08\u4f8b\u5982\u4e24\u79cd\u7ec6\u80de\u7c7b\u578b\u6216\u4e24\u79cd\u5904\u7406\u6761\u4ef6\uff09\u4e4b\u95f4\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u6bd4\u503c\u7684\u5bf9\u6570\u3002\u5bf9\u6570\u6298\u53e0\u53d8\u5316\u53ef\u4ee5\u53cd\u6620\u57fa\u56e0\u7684\u5dee\u5f02\u8868\u8fbe\u7a0b\u5ea6\uff0c\u6b63\u503c\u8868\u793a\u7b2c\u4e00\u7ec4\u6837\u672c\u4e2d\u57fa\u56e0\u8868\u8fbe\u66f4\u9ad8\uff0c\u8d1f\u503c\u8868\u793a\u7b2c\u4e8c\u7ec4\u6837\u672c\u4e2d\u57fa\u56e0\u8868\u8fbe\u66f4\u9ad8\u3002\u5e73\u5747\u5bf9\u6570\u6298\u53e0\u53d8\u5316\u662f\u5bf9\u6bcf\u4e2a\u57fa\u56e0\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u91cf\u53d6\u5e73\u5747\u540e\u518d\u8ba1\u7b97\u7684\u5bf9\u6570\u6298\u53e0\u53d8\u5316\uff0c\u5e38\u7528\u4e8e\u8f6c\u5f55\u7ec4\u5206\u6790\u6216\u5355\u7ec6\u80de\u5206\u6790\u4e2d\uff0c\u4f5c\u4e3a\u7b5b\u9009\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u7684\u4e00\u4e2a\u6807\u51c6\u3002<\/span><\/section>\n<section style=\"font-size: 16px;margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n<p style=\"text-wrap: wrap;\"><br \/><\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d<span style=\"color: rgb(255, 41, 65);\">\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"text-decoration: underline;color: rgb(255, 41, 65);font-size: 16px;\"><em><strong>\u6587\u4ef6\u7f16\u53f7\uff1a240116<\/strong><\/em><\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\"><strong><span style=\"color: rgb(255, 41, 65);\">\u679c\u7c89\u798f\u5229<\/span><\/strong><span style=\"color: rgb(0, 128, 255);\"><strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span><br \/><\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><span style=\"font-size: 16px;\">\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/span><\/p>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;font-size: 16px;background-color: rgb(255, 255, 255);\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 16px;\" rel=\"noopener\"><span style=\"font-size: 16px;\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/span><\/a><span style=\"font-family: "Times New Roman";text-indent: 0pt;letter-spacing: 0.034em;font-size: 16px;\">       <\/span><o:p style=\"font-family: "Times New Roman";font-size: 10.5pt;text-indent: 0pt;letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u5728\u4e86\u89e3\u5982\u4f55\u5206\u79bb\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u4e4b\u540e\uff0c\u6211\u4eec\u7ec8\u4e8e\u53ef\u4ee5\u5f00\u59cb\u671f\u5f85\u5df2\u4e45\u7684\u5dee\u5f02\u5206\u6790\u4e86\uff01<\/span>    <span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u7b2c\u4e00\u6b65\uff1a\u5206\u79bb\u80bf\u7624\u57fa\u8d28\u7c07<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">         <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u6839\u636e\u5c0f\u679c\u4e3a\u5927\u5bb6\u63d0\u4f9b\u7684\u4ee3\u7801\uff0c\u9996\u5148\u5bfc\u5165\u6240\u9700\u7684R\u5305\uff0c<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(255, 0, 0);\">\u8fd9\u4e00\u6b65\u4e2d\u4e3b\u8981\u7528\u5230\u7684\u662fSeurat\u548c scales\uff0c\u8fd9\u4e24\u4e2a\u5305\u5728\u5f80\u671f\u7684\u63a8\u9001\u4e2d\u6709\u8be6\u7ec6\u7684\u4ecb\u7ecd\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u5173\u6ce8\u5c0f\u679c\u5e76\u641c\u7d22\u54e6<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u3002<\/span><\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015212\" data-ratio=\"0.38981481481481484\" data-w=\"1080\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2024-01-21_\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u5206\u6790\u795e\u5668\uff013\u5206\u949f\u5e26\u4f60\u7528Seurat\u63ea\u51fa\u80bf\u7624\u201c\u81f4\u547d\u57fa\u56e0\u201d\uff01\/2_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png&wxfrom=5&wx_lazy=1&wx_co=1'\" \/>  <\/span><span style=\"font-size: 16px;font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">\u672c\u671f\u6240\u7528\u7684\u6570\u636e\u5c0f\u679c\u5df2\u7ecf\u51c6\u5907\u597d\u653e\u5728\u4e0b\u9762\u7684\u94fe\u63a5\u4e2d\u4e86\u54df~         <\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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\/12y5rnPGjJT-oVYyCQzzELw<\/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\uff1agbpc<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">        <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u8f93\u5165\u6570\u636e\u5982\u56fe\u6240\u793a\uff0c\u5c0f\u679c\u5df2\u7ecf\u5c06\u6240\u9700\u7684\u529f\u80fd\u51fd\u6570\u4ee5\u53ca\u53d8\u91cf\uff0c\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6570\u636e\u6574\u7406\u4e3aR\u6570\u636e\uff0c\u5927\u5bb6\u76f4\u63a5\u5bfc\u5165\u5373\u53ef\u4f7f\u7528<\/span>          <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"5.2000794\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"5.2000794\" style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015208\" data-ratio=\"0.5814814814814815\" data-type=\"png\" data-w=\"1080\" height=\"322 .1400146484375\" width=\"553 .739990234375\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ctp5Yibicegiaaiaec8t3JbibYsEWg.png?resize=553%2C322\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcXwIt7Vq537l53Sp3cmZfqvaVRJUC0ictp5Yibicegiaaiaec8t3JbibYsEWg\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><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;font-size: 16px;\"> <o:p> <\/o:p><\/span><span style=\"font-size: 16px;letter-spacing: 0.034em;\">    <\/span><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;letter-spacing: 0.034em;\"><\/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;\"># \u5bfc\u5165\u5305<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(Seurat)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(scales)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">save_dir = '\/results'<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fnm = paste0(save_dir,'\/seurat_object.RData')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">load(fnm)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u5b9a\u4e49\u80bf\u7624\u533a\u57df<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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\">tumor_stroma_clu <- function(SID){ fnm = paste<span class=\"code-snippet__number\">0<\/span>(save_dir,<span class=\"code-snippet__string\">'\/MIA\/A'<\/span>,SID,<span class=\"code-snippet__string\">'.xls'<\/span>) tmp1 = read.table(fnm,header = TRUE, stringsAsFactors = F, check.names=F) tms = c(<span class=\"code-snippet__string\">'Ep_1'<\/span>,<span class=\"code-snippet__string\">'Ep_2'<\/span>,<span class=\"code-snippet__string\">'Ep_3'<\/span>,<span class=\"code-snippet__string\">'Ep_4'<\/span>) N_clu = dim(tmp1)[<span class=\"code-snippet__number\">2<\/span>] TM_clu = c(<span class=\"code-snippet__string\">'100'<\/span>) <span class=\"code-snippet__comment\"># tumor clusters SM_clu = c('100') # stroma clustersfor (i in seq(1,length(tms))){for (j in seq(1,N_clu)){if (tmp1[tms[i],j]>10){ TM_clu = c(TM_clu,colnames(tmp1)[j]) } } } TM_clu = TM_clu[2:length(TM_clu)] TM_clu = unique(TM_clu) SM_clu = setdiff(colnames(tmp1),TM_clu)return(list(TM_clu,SM_clu))} <\/span><\/span><\/code><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u5c06\u6240\u6709\u80bf\u7624\u533a\u57df\u4f5c\u4e3a\u5143\u6570\u636e\u6c47\u96c6<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pool_TM = function(SOE,TM_clu){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> temp = SOE@meta.data$seurat_clusters<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> temp = as.character(temp)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for(i in seq(1,length(temp))){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if (temp[i] %in% TM_clu){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> temp[i] = 'tumor'<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> SOE@meta.data$pool_tumor = as.factor(temp)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">return(SOE)<\/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;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u5c06\u6240\u6709\u57fa\u8d28\u533a\u57df\u4f5c\u4e3a\u5143\u6570\u636e\u6c47\u96c6<\/span>    <\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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\">pool_SM = function(SOE,SM_clu){ temp = SOE@meta.data$seurat_clusters temp = as.character(temp)<span class=\"code-snippet__keyword\">for<\/span>(i in se<span class=\"code-snippet__string\">q(1,length(temp)<\/span>)){<span class=\"code-snippet__keyword\">if<\/span> (temp[i] %in% SM_clu){ temp[i] = <span class=\"code-snippet__string\">'stroma'<\/span> } } SOE@meta.data$pool_stroma = as.factor(temp)<span class=\"code-snippet__keyword\">return<\/span>(SOE)}          <\/span><\/code><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u5b9a\u4e49\u53d8\u91cf<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<pre class=\"code-snippet__js\" data-lang=\"ini\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SID = '4'<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SOE = sample4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">TS = tumor_stroma_clu(SID)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">TM_clu = unlist(TS[1])<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SM_clu = unlist(TS[2])<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SOE = pool_TM(SOE,TM_clu)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">sample4 = pool_SM(SOE,SM_clu)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u50a8\u5b58Seurat \u9879\u76ee<\/span>    <\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fnm = paste0(save_dir,'\/seurat_object_TM_SM.RData')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">save(sample4,sample5,sample10,sample12, file = fnm) # Save the object<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">\u7b2c\u4e8c\u6b65\uff1a\u7ed8\u5236\u80bf\u7624\u8f6e\u5ed3<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u5728\u7b2c\u4e94\u6b65\u7684\u57fa\u7840\u4e0a\uff0c\u6211\u4eec\u9700\u8981\u989d\u5916\u5bfc\u5165imager\uff0cmagick\uff0cstringr\u8fd9\u4e09\u4e2a\u5305\uff0c\u5f15\u7528\u7b2c\u4e94\u6b65\u4e2d\u8bbe\u7f6e\u7684\u80bf\u7624\u7c07\u5b9a\u4f4d\u51fd\u6570\uff0c\u8fdb\u800c\u7ed8\u5236\u80bf\u7624\u7c07\u8f6e\u5ed3\uff0c\u7ed8\u5236\u7684\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff0c\u5206\u522b\u662f\u56db\u4e2a\u6837\u672c\u7684\u80bf\u7624\u7c07\u8f6e\u5ed3\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">        <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\"># \u5bfc\u5165\u5305<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(magick)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">library(stringr)<span style=\"color: rgba(0, 0, 0, 0.9);text-align: justify;font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">      <\/span><o:p style=\"color: rgba(0, 0, 0, 0.9);text-align: justify;font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\"> <\/o:p><\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u4fdd\u5b58\u7ed3\u679c\u6587\u4ef6<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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=\"javascript\"><code><span class=\"code-snippet_outer\">folder = paste0(save_dir,<span class=\"code-snippet__string\">'\/map_tumor_region'<\/span>)<span class=\"code-snippet__keyword\">if<\/span> (!file.exists(folder)){ dir.create(folder)}folder1 = paste0(save_dir,<span class=\"code-snippet__string\">'\/map_tumor_outline'<\/span>)<span class=\"code-snippet__keyword\">if<\/span> (!file.exists(folder1)){ dir.create(folder1) } <\/span><\/code><\/pre>\n<\/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: rgb(0, 112, 192);font-size: 16px;\"><o:p><\/o:p><\/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;\">## \u627e\u5230\u80bf\u7624\u7c07<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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\">tum_clu <- function(SID){ fnm = paste<span class=\"code-snippet__number\">0<\/span>(save_dir,<span class=\"code-snippet__string\">'\/MIA\/A'<\/span>,SID,<span class=\"code-snippet__string\">'.xls'<\/span>) tmp1 = read.table(fnm,header = TRUE, stringsAsFactors = F, check.names=F) tms = c(<span class=\"code-snippet__string\">'Ep_1'<\/span>,<span class=\"code-snippet__string\">'Ep_2'<\/span>,<span class=\"code-snippet__string\">'Ep_3'<\/span>,<span class=\"code-snippet__string\">'Ep_4'<\/span>)<span class=\"code-snippet__comment\"># tms = c('T')# tms = c('FB_1','FB_2','FB_3') N_clu = dim(tmp1)[2] TM_clu = c('100')for (i in seq(1,length(tms))){for (j in seq(1,N_clu)){if (tmp1[tms[i],j]>10){ TM_clu = c(TM_clu,colnames(tmp1)[j]) } } } TM_clu = TM_clu[2:length(TM_clu)] TM_clu = unique(TM_clu)return(TM_clu) } <\/span><\/span><\/code><\/pre>\n<\/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: rgb(0, 112, 192);font-size: 16px;\"><o:p><\/o:p><\/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;\">## \u7ed8\u5236\u80bf\u7624\u533a\u57df<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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=\"php\"><code><span class=\"code-snippet_outer\">map_tumor <- <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(SID,SOE,topleft,topright,bottomleft,bottomright,im,size = <span class=\"code-snippet__number\">7<\/span>)<\/span><\/span>{ tumor_clu = tum_clu(SID) tmp0 = SOE@meta.data$seurat_cluster nspots = length(tmp0) mycols1 <- c(rep(<span class=\"code-snippet__string\">'NA'<\/span>,length(tmp0)))<span class=\"code-snippet__keyword\">for<\/span> (i in seq(<span class=\"code-snippet__number\">1<\/span>,nspots)){<span class=\"code-snippet__keyword\">if<\/span> (tmp0[i] %in% tumor_clu){ mycols1[i] = <span class=\"code-snippet__string\">'black'<\/span> } } delta_x = mean(abs(topright[<span class=\"code-snippet__number\">1<\/span>]-topleft[<span class=\"code-snippet__number\">1<\/span>]),abs(bottomright[<span class=\"code-snippet__number\">1<\/span>]-bottomleft[<span class=\"code-snippet__number\">1<\/span>]))\/<span class=\"code-snippet__number\">32<\/span> delta_y = mean(abs(topright[<span class=\"code-snippet__number\">2<\/span>]-bottomright[<span class=\"code-snippet__number\">2<\/span>]),abs(topleft[<span class=\"code-snippet__number\">2<\/span>]-bottomleft[<span class=\"code-snippet__number\">2<\/span>]))\/<span class=\"code-snippet__number\">34<\/span> adjust_x = <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(step)<\/span><\/span>{<span class=\"code-snippet__keyword\">return<\/span>((step<span class=\"code-snippet__number\">-1<\/span>)*(bottomleft[<span class=\"code-snippet__number\">1<\/span>]-topleft[<span class=\"code-snippet__number\">1<\/span>])\/<span class=\"code-snippet__number\">34<\/span>)} adjust_y = <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(step)<\/span><\/span>{<span class=\"code-snippet__keyword\">return<\/span>((step<span class=\"code-snippet__number\">-1<\/span>)*(topright[<span class=\"code-snippet__number\">2<\/span>]-topleft[<span class=\"code-snippet__number\">2<\/span>])\/<span class=\"code-snippet__number\">32<\/span>)} tmp = <span class=\"code-snippet__keyword\">as<\/span>.matrix(GetAssayData(object = SOE, assay = <span class=\"code-snippet__string\">\"SCT\"<\/span>, slot = <span class=\"code-snippet__string\">\"scale.data\"<\/span>)) tmp1 = colnames(tmp)<span class=\"code-snippet__keyword\">if<\/span> (nchar(SID)==<span class=\"code-snippet__number\">1<\/span>){ tmp1 = substr(tmp1,<span class=\"code-snippet__number\">4<\/span>,<span class=\"code-snippet__number\">100<\/span>) } <span class=\"code-snippet__keyword\">else<\/span>{ tmp1 = substr(tmp1,<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">100<\/span>) } colnames(tmp) = tmp1 x = <span class=\"code-snippet__keyword\">as<\/span>.numeric(unlist(lapply(tmp1, <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(x)<\/span><\/span>{strsplit(x,<span class=\"code-snippet__string\">\"x\"<\/span>)[[<span class=\"code-snippet__number\">1<\/span>]][<span class=\"code-snippet__number\">1<\/span>]}))) y = <span class=\"code-snippet__keyword\">as<\/span>.numeric(unlist(lapply(tmp1, <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(x)<\/span><\/span>{strsplit(x,<span class=\"code-snippet__string\">\"x\"<\/span>)[[<span class=\"code-snippet__number\">1<\/span>]][<span class=\"code-snippet__number\">2<\/span>]}))) d = data.frame(x,y) filenm = paste0(folder,<span class=\"code-snippet__string\">'\/A'<\/span>,SID,<span class=\"code-snippet__string\">'_tumor.png'<\/span>) png(filenm, width = dim(im)[<span class=\"code-snippet__number\">1<\/span>], height = dim(im)[<span class=\"code-snippet__number\">2<\/span>]) par(mar = c(<span class=\"code-snippet__number\">0<\/span>,<span class=\"code-snippet__number\">0<\/span>,<span class=\"code-snippet__number\">0<\/span>,<span class=\"code-snippet__number\">0<\/span>)) <span class=\"code-snippet__comment\"># set zero margins on all 4 sides plot(x = NULL, y = NULL, xlim = c(0,dim(im)[1]), ylim = c(0,dim(im)[2]), pch = '', xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xaxs = 'i', yaxs = 'i', bty = 'n') # plot empty figure# rasterImage(im, xleft = 0, ybottom = 0, xright = dim(im)[1], ytop = dim(im)[2]) points(topleft[1]+(d[,1]-1)*delta_x+apply(d,1,function(x){return(adjust_x(x[2]))}), topleft[2]-(d[,2]-1)*delta_y+apply(d,1,function(x){return(adjust_y(x[1]))}), col=mycols1,pch=15,cex=size) dev.off()}         <\/span><\/span><\/code><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u5b9a\u4e49\u53d8\u91cf<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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=\"makefile\"><code><span class=\"code-snippet_outer\">SID = '4'SOE = sample4fnm = paste0(image_dir,'\/Sample_',SID,'_ds.jpg') <span class=\"code-snippet__comment\"># downsample to 0.25xim = load.image(fnm)# plot(im)xd = dim(im)[1]yd = dim(im)[2]topleft = c(58,yd-50)topright = c(1412,yd-64)bottomleft = c(48,yd-1512)bottomright = c(1400,yd-1524)map_tumor(SID,SOE,topleft,topright,bottomleft,bottomright,im,size=8.5)<\/span><\/span><\/code><\/pre>\n<\/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;\">*\u5176\u4f59\u4e09\u4e2a\u6837\u672c\u8fdb\u884c\u76f8\u540c\u5904\u7406<\/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;font-size: 16px;\">      <o:p> <\/o:p><\/span><span style=\"letter-spacing: 0.034em;font-size: 16px;\">    <\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><o:page><\/o:page><\/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;\">## \u7ed8\u5236\u80bf\u7624\u8f6e\u5ed3<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"markdown\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">files1 = list.files(folder)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (i in seq(1,length(files1))){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> directory = paste0(folder,'\/',files1[i])<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> sample_id = str_split(files1[i],'.png')[[1]][1]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fig <- image_read(directory)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> # print(fig)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fig = fig %>% image_morphology('EdgeOut', 'Octagon') %>% image_negate() # edge detection<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> filenm = paste0(folder1,'\/',sample_id,'_outline.png')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> image_write(fig, filenm)<\/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;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"24.000366\" height=\"35.867214\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"24.000366\" height=\"35.867214\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015204\" data-ratio=\"0.9416846652267818\" data-type=\"png\" data-w=\"463\" height=\"435.4733581542969\" width=\"462.4761962890625\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2024-01-21_\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u5206\u6790\u795e\u5668\uff013\u5206\u949f\u5e26\u4f60\u7528Seurat\u63ea\u51fa\u80bf\u7624\u201c\u81f4\u547d\u57fa\u56e0\u201d\uff01\/4_bN3K2KUdPNJGUynD2K3uPNYia9tThQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcgVW903rqmezeVpWaOCQU9zrrvibN3K2KUdPNJGUynD2K3uPNYia9tThQ\/640?wx_fmt=png'\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\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\u662f\u6211\u4eec\u4f9d\u636e\u80bf\u7624\u7684\u8f6e\u5ed3\u8fdb\u884c\u7684\u7ed8\u56fe\uff0c\u53ef\u4ee5\u975e\u5e38\u6e05\u6670\u7684\u770b\u5230\u80bf\u7624\u7684\u754c\u9650\uff0c\u63a5\u7740\u6211\u4eec\u9700\u8981\u627e\u51fa\u4e2a\u4f53\u7684\u57fa\u56e0\uff0c\u7136\u540e\u5c06\u5176\u4e0e\u80bf\u7624\u7684\u8f6e\u5ed3\u8fdb\u884c\u6bd4\u5bf9\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">        <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u7b2c\u4e09\u6b65\uff1a\u4e0e\u4e2a\u4f53\u57fa\u56e0\u6bd4\u5bf9<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">        <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5e26\u7740\u5927\u5bb6\u6765\u627e\u51fascRNA\u4e2d\u7684\u7279\u5f81\u57fa\u56e0\uff0c\u4f9d\u636e\u7ed9\u51fa\u7684\u4ee3\u7801\uff0c\u5c06\u80bf\u7624\u4e0e\u57fa\u56e0\u76f8\u6bd4\u5bf9\uff0c\u5c31\u53ef\u4ee5\u7ed8\u5236\u51fa\u4e0b\u65b9\u7684\u56fe\uff0c\u5f53\u7136\uff0c\u4e0b\u65b9\u7684\u56db\u5e45\u56fe\u53ea\u5c55\u793a\u4e86COL1A1\u8fd9\u4e2a\u57fa\u56e0\u4e0e\u56db\u4e2a\u6837\u672c\u7684\u4e4b\u95f4\u7684\u6620\u5c04\u5173\u7cfb\uff0c\u5269\u4f59\u7684\u57fa\u56e0\u4e0e\u80bf\u7624\u7c07\u7684\u6620\u5c04\u5173\u7cfb\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u81ea\u5df1\u5728\u7ed3\u679c\u6587\u4ef6\u4e2d\u627e\u4e00\u627e\u54e6\u3002<\/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;font-size: 16px;\">         <o:p> <\/o:p><\/span><span style=\"letter-spacing: 0.034em;font-size: 16px;\">    <\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><o:page><\/o:page><\/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;\">## \u8bbe\u5b9a\u80bf\u7624\uff0c\u57fa\u8d28\u57fa\u56e0<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">geneb = c('POSTN','CD36','ACTA2','VIM','S100A4','PDGFRB','PDGFRA',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">'FAP','COL1A1','WFDC2','MUC16','CLDN4')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> <\/span><\/span><\/code><\/section><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u6bd4\u5bf9\u57fa\u56e0<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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=\"php\"><code><span class=\"code-snippet_outer\">map_gene <- <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">function<\/span><span class=\"code-snippet__params\">(gene,SID,SOE,RorG,topleft,topright,bottomleft,bottomright,im)<\/span><\/span>{ fnm = paste0(save_dir,<span class=\"code-snippet__string\">'\/map_tumor_outline\/A'<\/span>,SID,<span class=\"code-snippet__string\">'_tumor_outline.png'<\/span>) <span class=\"code-snippet__comment\"># downsample to 0.25x im1 = load.image(fnm) delta_x = mean(abs(topright[1]-topleft[1]),abs(bottomright[1]-bottomleft[1]))\/32 delta_y = mean(abs(topright[2]-bottomright[2]),abs(topleft[2]-bottomleft[2]))\/34 adjust_x = function(step){return((step-1)*(bottomleft[1]-topleft[1])\/34)} adjust_y = function(step){return((step-1)*(topright[2]-topleft[2])\/32)} tmp = as.matrix(GetAssayData(object = SOE, assay = \"SCT\", slot = \"scale.data\")) tmp1 = colnames(tmp)if (nchar(SID)==1){ tmp1 = substr(tmp1,4,100) } else{ tmp1 = substr(tmp1,5,100) } colnames(tmp) = tmp1 x = as.numeric(unlist(lapply(tmp1, function(x){strsplit(x,\"x\")[[1]][1]}))) y = as.numeric(unlist(lapply(tmp1, function(x){strsplit(x,\"x\")[[1]][2]}))) d = data.frame(x,y) all_genes = rownames(tmp) id = 0for (i in seq(1,length(all_genes),by = 1)){if (all_genes[i] == gene){ id = ibreak}}if (id == 0){print('No matched genes!') } data_1 = tmp[id,] vec = (data_1-min(data_1))\/(max(data_1)-min(data_1))require(grDevices) R = 'brown' G = 'darkgreen' B = 'darkblue'if (RorG==1){ mycols <- colorRamp(c('darkgray','white','lightcoral','red'), space = \"Lab\")(vec) } else if (RorG==2){ mycols <- colorRamp(c(\"white\",G), space = \"Lab\")(vec) } else { mycols <- colorRamp(c(\"white\",B), space = \"Lab\")(vec) } mycols <- rgb(mycols[,1], mycols[,2], mycols[,3], maxColorValue = 255) # Transform the rgb colors in hexadecimal format filenm = paste0(folder,'\/A',SID,'_',gene,'_with_tumor_gray.png') png(filenm, width = 512, height = 512) par(mar = c(0,0,0,0)) # set zero margins on all 4 sides plot(x = NULL, y = NULL, xlim = c(0,dim(im)[1]), ylim = c(0,dim(im)[2]), pch = '', xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xaxs = 'i', yaxs = 'i', bty = 'n') # plot empty figure rasterImage(im1, xleft = 0, ybottom = 0, xright = dim(im1)[1], ytop = dim(im1)[2]) points(topleft[1]+(d[,1]-1)*delta_x+apply(d,1,function(x){return(adjust_x(x[2]))}), topleft[2]-(d[,2]-1)*delta_y+apply(d,1,function(x){return(adjust_y(x[1]))}), col=mycols,pch=20,cex=3) title(gene, line = -1) dev.off()# print(gene)}##SID = '4'SOE = sample4fnm = paste0(image_dir,'\/Sample_',SID,'_ds.jpg') # downsample to 0.25xim = load.image(fnm)# plot(im)xd = dim(im)[1]yd = dim(im)[2]topleft = c(58,yd-50)topright = c(1412,yd-64)bottomleft = c(48,yd-1512)bottomright = c(1400,yd-1524) isRorG = 1gene = genebgenes = rownames(SOE@assays$SCT)gene = intersect(gene,genes)for (i in seq(1,length(gene))){ map_gene(gene[i],SID,SOE,isRorG,topleft,topright,bottomleft,bottomright,im)}         <\/span><\/span><\/code><\/pre>\n<\/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;\"><o:p><\/o:p><\/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;\">## \u7ed8\u5236\u989c\u8272\u6761\u5e26<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"xml\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">color.bar <- function(lut, min=0, max=1, nticks=11, ticks=seq(min, max, len=nticks), title='') {<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">scale = (length(lut)-1)\/(max-min)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">filenm = paste0(folder,'\/color_bar.png')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">png(filenm, width = 170, height = 500)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">plot(c(0,10), c(min,max), type='n', bty='n', xaxt='n', xlab='', yaxt='n', ylab='', main=title)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">axis(2, ticks, las=1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (i in 1:(length(lut)-1)) {<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">y = (i-1)\/scale + min<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">rect(0,y,10,y+1\/scale, col=lut[i], border=NA)<\/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\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">color.bar(colorRampPalette(c('darkgray','white','lightcoral','red'))(100))<\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\">          <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"23.533691\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"23.533691\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015207\" data-ratio=\"0.7730769230769231\" data-type=\"png\" data-w=\"520\" height=\"401 .6731262207031\" width=\"519 .141845703125\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_AxSVynZ9RE5aweDPc2emW2icn3kvrg.png?resize=519%2C401\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcuAlqqyicBUPUloaEHZAEGDCL42AxSVynZ9RE5aweDPc2emW2icn3kvrg\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\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\u662f\u6211\u4eec\u5c06\u4e2a\u4f53\u57fa\u56e0\u4e0e\u80bf\u7624\u7684\u8f6e\u5ed3\u8fdb\u884c\u6bd4\u5bf9\u4e4b\u540e\u7684\u7ed3\u679c\uff0c\u6709\u5f88\u591a\u7684\u7ed3\u679c\u56fe\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u53ea\u5217\u51fa\u4e86\u4e00\u4e2a\u57fa\u56e0\u7684\u6bd4\u5bf9\u56fe\uff0c\u53ef\u4ee5\u770b\u51fa\u5728\u56db\u4e2a\u6837\u672c\u4e2d\uff0cCOL1A1\u57fa\u56e0\u7684\u8868\u8fbe\u662f\u975e\u5e38\u4e30\u5bcc\u7684\uff0c\u56fe\u4e2d\u7684\u7ea2\u8272\u533a\u57df\u4ee3\u8868\u9ad8\u8868\u8fbe\u7684\u533a\u57df\uff0c\u7070\u8272\u7684\u5219\u4ee3\u8868\u4f4e\u8868\u8fbe\u7684\u533a\u57df\u3002<\/span>    <span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u7b2c\u56db\u6b65\uff1a\u5c06\u9009\u5b9a\u7684\u7c07\uff08\u4f8b\u5982CAF-\u764c\u75c7\u76f8\u5173\u6210\u7ea4\u7ef4\u7ec6\u80de\uff09\u6620\u5c04\u5230\u5177\u6709\u80bf\u7624\u8f6e\u5ed3\u7684\u56fe\u50cf\u4e0a<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">         <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u53ea\u6709\u80bf\u7624\u7684\u8f6e\u5ed3\u662f\u65e0\u6cd5\u8fdb\u884c\u5206\u6790\u7684\uff0c\u56e0\u6b64\uff0c\u5fc5\u987b\u8981\u5c06\u7279\u5b9a\u7684\u80bf\u7624\u7c07\u7ed8\u5236\u5230\u80bf\u7624\u7684\u8f6e\u5ed3\u4e0a\uff0c\u6211\u4eec\u9700\u8981\u5bfc\u5165\u989d\u5916\u7684\u5305\uff1adplyr\u3002\u7136\u540e\u6309\u7167\u4ee3\u7801\u5c06\u4e0e\u764c\u75c7\u76f8\u5173\u7684\u6210\u7ea4\u7ef4\u7ec6\u80de\uff08CAF\uff09\u6bd4\u5bf9\u81f3\u80bf\u7624\u8f6e\u5ed3\u4e0a\uff0c\u5728\u8bbe\u7f6e\u597d\u56db\u4e2a\u6837\u672c\u7684\u53c2\u6570\u540e\uff0c\u5373\u53ef\u5f97\u5230\u7ed3\u679c\u56fe\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">         <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">## \u5c06\u80bf\u7624\u7684\u8f6e\u5ed3\u6bd4\u5bf9\u81f3\u764c\u75c7\u76f8\u5173\u7684\u6210\u7ea4\u7ef4\u7ec6\u80de<\/span><\/section>\n<p><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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">map_clusters <- function(clusters,fib_clu,tum_clu,SID,SOE,topleft,topright,bottomleft,bottomright,im){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fnm = paste0(save_dir,'\/map_tumor_outline\/A',SID,'_tumor_outline.png')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> im = load.image(fnm)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> delta_x = mean(abs(topright[1]-topleft[1]),abs(bottomright[1]-bottomleft[1]))\/32<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> delta_y = mean(abs(topright[2]-bottomright[2]),abs(topleft[2]-bottomleft[2]))\/34<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> adjust_x = function(step){return((step-1)*(bottomleft[1]-topleft[1])\/34)}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> adjust_y = function(step){return((step-1)*(topright[2]-topleft[2])\/32)}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> tmp = SOE@meta.data$seurat_cluster<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> Nclu = length(levels(tmp))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> nspots = length(tmp)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mycolpalette1 = c('orange','paleturquoise4','orchid','seagreen2','slateblue1','yellow')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mycolpalette = c('red','darkgreen','blue','cyan','black','yellow')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mycols <- c(rep(NA,length(tmp)))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (i in seq(1,nspots)){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (j in seq(1,length(fib_clu))){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if ((as.character(tmp[i]) == fib_clu[j]) && (as.character(tmp[i]) %in% clusters)){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> mycols[i] = mycolpalette1[j]<\/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;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> }<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> filenm = paste0(save_dir,'\/map_CAF_clusters','\/A',SID,'_CAF.png')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> png(filenm, width = 512, height = 512)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> par(mar = c(0,0,0,0),'bg'='lightgray') # set zero margins on all 4 sides<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> plot(x = NULL, y = NULL, xlim = c(0,dim(im)[1]), ylim = c(0,dim(im)[2]), pch = '',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> xaxt = 'n', yaxt = 'n', xlab = '', ylab = '', xaxs = 'i', yaxs = 'i', <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> bty = 'n') # plot empty figure<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> rasterImage(im, xleft = 0, ybottom = 0, xright = dim(im)[1], ytop = dim(im)[2])<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> points(topleft[1]+(d[,1]-1)*delta_x+apply(d,1,function(x){return(adjust_x(x[2]))}),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> topleft[2]-(d[,2]-1)*delta_y+apply(d,1,function(x){return(adjust_y(x[1]))}),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> col=mycols,pch=15,cex=2)<\/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\"><span style=\"font-size: 16px;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">##A4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SID = '4'<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">SOE = sample4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fnm = paste0(image_dir,'\/Sample_',SID,'_ds.jpg')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">im = load.image(fnm)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">plot(im)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">xd = dim(im)[1]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">yd = dim(im)[2] <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">topleft = c(58,yd-50)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">topright = c(1412,yd-64)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">bottomleft = c(48,yd-1512)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">bottomright = c(1400,yd-1524)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">delta_x = mean(abs(topright[1]-topleft[1]),abs(bottomright[1]-bottomleft[1]))\/32<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">delta_y = mean(abs(topright[2]-bottomright[2]),abs(topleft[2]-bottomleft[2]))\/34<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">adjust_x = function(step){return((step-1)*(bottomleft[1]-topleft[1])\/34)}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">adjust_y = function(step){return((step-1)*(topright[2]-topleft[2])\/32)}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tmp = as.matrix(GetAssayData(object = SOE, assay = \"SCT\", slot = \"data\"))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tmp1 = colnames(tmp)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tmp1 = substr(tmp1,4,100)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">colnames(tmp) = tmp1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">x = as.numeric(unlist(lapply(tmp1, function(x){strsplit(x,\"x\")[[1]][1]})))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">y = as.numeric(unlist(lapply(tmp1, function(x){strsplit(x,\"x\")[[1]][2]})))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">d = data.frame(x,y)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">fib_clu = c(\"0\",\"1\",\"3\",\"4\",\"6\",\"7\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">tum_clu = c(\"2\",\"5\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">clusters = c('0','7')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">map_clusters(clusters,fib_clu,tum_clu,SID,SOE,topleft,topright,bottomleft,bottomright,im)<\/span><\/span><\/code><\/section><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\">          <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"5.0000763\" height=\"34.467194\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"5.0000763\" height=\"34.467194\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015206\" data-ratio=\"0.8168103448275862\" data-type=\"png\" data-w=\"464\" height=\"378.943115234375\" width=\"463.54461669921875\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2024-01-21_\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u5206\u6790\u795e\u5668\uff013\u5206\u949f\u5e26\u4f60\u7528Seurat\u63ea\u51fa\u80bf\u7624\u201c\u81f4\u547d\u57fa\u56e0\u201d\uff01\/6_1g1xpKopep3R6Dst6mJibrZFSHwuCA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcEy5SicsCmwCibbgJYDs4DJhrYQ81g1xpKopep3R6Dst6mJibrZFSHwuCA\/640?wx_fmt=png'\" \/><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;\"><br \/><\/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;\">\u6211\u4eec\u5c06\u81ea\u5df1\u9009\u5b9a\u7684\u80bf\u7624\u7c07\uff08CAF\uff09\u6295\u5c04\u5230\u4e4b\u524d\u7ed8\u51fa\u7684\u8f6e\u5ed3\u56fe\u4e0a\uff0c\u5373\u53ef\u770b\u5230\u7279\u5b9a\u7684\u7c07\u5728\u6574\u4e2a\u80bf\u7624\u8f6e\u5ed3\u4e2d\u7684\u5206\u5e03\uff0c\u6700\u540e\u6211\u4eec\u8fd8\u9700\u8981\u5bf9\u6240\u7814\u7a76\u7684\u7c07\u548c\u6574\u4e2a\u80cc\u666f\u7c07\u8fdb\u884c\u57fa\u56e0\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u770b\u770b\u7a76\u7adf\u5728\u7279\u5b9a\u7684\u80bf\u7624\u7c07\u4e2d\u4ec0\u4e48\u6837\u7684\u57fa\u56e0\u662f\u8868\u8fbe\u6700\u4e30\u5bcc\u7684\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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;\">\u7b2c\u4e94\u6b65\uff1a\u53ef\u89c6\u5316\u7c07logFC<\/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;\">\u5728\u8fd9\u4e00\u6b65\uff0c\u6211\u4eec\u5c31\u8981\u7528\u5230\u5728\u6587\u7ae0\u4e00\u5f00\u59cb\u63d0\u5230\u7684<\/span><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;\">avg_logFC\u4e86\uff0c\u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u662f\u5426\u8fd8\u8bb0\u5f97\u5462\uff1f\u5982\u679c\u5fd8\u8bb0\u7684\u8bdd\u8d76\u5feb\u8fd4\u56de\u53bb\u770b\u4e00\u4e0b~<\/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: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u4e3a\u4e86\u8ba9\u6211\u4eec\u7684\u56fe\u7247\u66f4\u52a0\u591a\u5f69\uff0c\u6211\u4eec\u9700\u8981\u65b0\u5bfc\u5165\u4e24\u4e2aR\u5305\uff1agplots\uff0cRcolorBrewer\u3002\u7136\u540e\u63d0\u53d6\u4e0d\u540c\u7c07\u4e2d\u7684\u6700\u9ad8\u548c\u6700\u4f4e\u7684\u5dee\u5f02\u5316\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u5e76\u8bb0\u5f55\u4ed6\u4eec\u7684\u6570\u91cf\u3002\u63a5\u7740<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(17, 17, 17);\">\u63d0\u53d6\u51fa\u4e0d\u540c\u57fa\u56e0\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u5dee\u5f02\u8868\u8fbe\u7a0b\u5ea6\uff0c\u4e5f\u5c31\u662f<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;\">\u5e73\u5747\u5bf9\u6570\u6298\u53e0\u53d8\u5316-avg_logFC\uff0c\u5728\u8fd9\u4e2a\u57fa\u7840\u4e0a\uff0c<\/span><span style=\"font-family: \u7b49\u7ebf;font-variant: normal;text-transform: none;color: rgb(17, 17, 17);\">\u6839\u636e\u5e73\u5747\u5bf9\u6570\u6298\u53e0\u53d8\u5316\u7684\u76f8\u5173\u6027\uff0c\u5bf9\u57fa\u56e0\u548c\u6837\u672c\u8fdb\u884c\u805a\u7c7b\u3002\u6700\u540e\uff0c\u9009\u62e9\u5177\u6709\u5dee\u5f02\u6027\u7684\u57fa\u56e0\uff0c\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u5c31\u53ef\u4ee5\u5f97\u5230\u4e0b\u9762\u7684\u4e24\u5e45\u56fe\u3002<\/span>    <span style=\"font-family: "Times New Roman";letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: "Times New Roman";font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: -apple-system;font-variant: normal;text-transform: none;color: rgb(17, 17, 17);\"># \u63d0\u53d6\u51fa\u57fa\u56e0\u7684\u5dee\u5f02\u8868\u8fbe\u4fe1\u606f<\/span><\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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\">genes = c()clusters = c()<span class=\"code-snippet__keyword\">for<\/span> (i in se<span class=\"code-snippet__string\">q(1,length(files)<\/span>)){ fnm = files[i] clu = unlist(strsplit(fnm,<span class=\"code-snippet__string\">'.x'<\/span>))[<span class=\"code-snippet__number\">1<\/span>] tmp1 = read.table(paste<span class=\"code-snippet__number\">0<\/span>(dir1,<span class=\"code-snippet__string\">'\/'<\/span>,fnm),header = TRUE, stringsAsFactors = F, check.names=F) tmp1 = tmp1[<span class=\"code-snippet__keyword\">abs<\/span>(tmp1$avg_logFC)><span class=\"code-snippet__number\">0<\/span>.<span class=\"code-snippet__number\">15<\/span>,] tmp1 = tmp1[tmp1$p_val<<span class=\"code-snippet__number\">0<\/span>.<span class=\"code-snippet__number\">01<\/span>,] genes = c(genes,tmp1$gene[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">20<\/span>]) temp = tmp1[order(tmp1$avg_logFC,decreasing = FALSE),] genes = c(genes,temp$gene[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">20<\/span>]) clusters= c(clusters,clu)}genes = unique(genes)df = data.frame(matrix(<span class=\"code-snippet__number\">0<\/span>, ncol = <span class=\"code-snippet__keyword\">length<\/span>(clusters), nrow = <span class=\"code-snippet__keyword\">length<\/span>(genes)))row.names(df) = genescolnames(df) = clustersfor (i in se<span class=\"code-snippet__string\">q(1,length(files)<\/span>)){ fnm = files[i] tmp1 = read.table(paste<span class=\"code-snippet__number\">0<\/span>(dir1,<span class=\"code-snippet__string\">'\/'<\/span>,fnm),header = TRUE, stringsAsFactors = F, check.names=F)<span class=\"code-snippet__keyword\">for<\/span> (j in se<span class=\"code-snippet__string\">q(1,length(genes)<\/span>)){<span class=\"code-snippet__keyword\">if<\/span> (genes[j] %in% tmp1$gene){ df[genes[j],i] = tmp1$avg_logFC[tmp1$gene==genes[j]] } }}my_palette <- colorRampPalette(brewer.pal(<span class=\"code-snippet__number\">10<\/span>, <span class=\"code-snippet__string\">\"RdBu\"<\/span>))(<span class=\"code-snippet__number\">256<\/span>)data = data.matrix(df) <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;\">## \u6839\u636e\u6700\u8fdc\u7684\u4e24\u4e2a\u5143\u7d20\u4e4b\u95f4\u7684\u8ddd\u79bb\u6765\u5408\u5e76\u4e0d\u540c\u7684\u7c07<\/span>    <\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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=\"kotlin\"><code><span class=\"code-snippet_outer\">hr <- hclust(<span class=\"code-snippet__keyword\">as<\/span>.dist(<span class=\"code-snippet__number\">1<\/span>-cor(t(<span class=\"code-snippet__keyword\">data<\/span>), method=<span class=\"code-snippet__string\">\"spearman\"<\/span>)), method=<span class=\"code-snippet__string\">\"complete\"<\/span>)hc <- hclust(<span class=\"code-snippet__keyword\">as<\/span>.dist(<span class=\"code-snippet__number\">1<\/span>-cor(<span class=\"code-snippet__keyword\">data<\/span>, method=<span class=\"code-snippet__string\">\"spearman\"<\/span>)), method=<span class=\"code-snippet__string\">\"complete\"<\/span>)<span class=\"code-snippet__keyword\">data<\/span>[<span class=\"code-snippet__keyword\">data<\/span><(-<span class=\"code-snippet__number\">1<\/span>)] = -<span class=\"code-snippet__number\">1<\/span><span class=\"code-snippet__keyword\">data<\/span>[<span class=\"code-snippet__keyword\">data<\/span>><span class=\"code-snippet__number\">1<\/span>] = <span class=\"code-snippet__number\">1f<\/span>ilename = paste0(folder,<span class=\"code-snippet__string\">'\/avg_logFC_heatmap_spearman.pdf'<\/span>)pdf(filename,<span class=\"code-snippet__number\">12<\/span>,<span class=\"code-snippet__number\">12<\/span>)heatmap.2(<span class=\"code-snippet__keyword\">data<\/span>, col = rev(my_palette), Rowv=<span class=\"code-snippet__keyword\">as<\/span>.dendrogram(hr), Colv=<span class=\"code-snippet__keyword\">as<\/span>.dendrogram(hc), trace=<span class=\"code-snippet__string\">\"none\"<\/span>, scale = <span class=\"code-snippet__string\">\"none\"<\/span>, density.info=<span class=\"code-snippet__string\">\"none\"<\/span>, margins=c(<span class=\"code-snippet__number\">5<\/span>,<span class=\"code-snippet__number\">6<\/span>), lhei=c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">8<\/span>), lwid=c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">4<\/span>), keysize=<span class=\"code-snippet__number\">0.2<\/span>, key.par = list(cex=<span class=\"code-snippet__number\">0.5<\/span>), cexRow=<span class=\"code-snippet__number\">0.9<\/span>,cexCol=<span class=\"code-snippet__number\">1.2<\/span>,srtCol=<span class=\"code-snippet__number\">90<\/span>, # rotate column label key.title = <span class=\"code-snippet__string\">'avg_logFC'<\/span>, key.xlab = <span class=\"code-snippet__string\">'avg_logFC'<\/span>)dev.off()  <\/span><\/code><\/pre>\n<\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 16px;\"><o:p><\/o:p><\/span><\/section>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 16px;\">## \u4e3aCAF\u7ed8\u5236\u53ef\u89c6\u5316\u7684\u9009\u62e9\u7684\u57fa\u56e0<\/span><span style=\"font-family: "Times New Roman";font-size: 16px;letter-spacing: 0.034em;\">       <\/span><o:p style=\"font-family: "Times New Roman";font-size: 16px;letter-spacing: 0.034em;\"> <\/o:p><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">genes = c('ACTA2','S100A4','FAP','VIM','PDGFRB','PDGFRA','CD36','POSTN','COL1A1')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">CAF_clusters = c(\"A4_c0\", \"A4_c1\", \"A4_c3\", \"A4_c4\", \"A4_c6\", \"A4_c7\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"A5_c0\", \"A5_c1\", \"A5_c2\", \"A5_c3\", \"A5_c4\", \"A5_c6\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"A10_c0\", \"A10_c1\", \"A10_c4\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">\"A12_c2\", \"A12_c3\", \"A12_c4\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">df = data.frame(matrix(0, ncol = length(CAF_clusters), nrow = length(genes)))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">row.names(df) = genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">colnames(df) = CAF_clusters<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (i in seq(1,length(CAF_clusters))){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> fnm = paste0(dir1,'\/',CAF_clusters[i],'.xls')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> tmp1 = read.table(fnm, header = TRUE, stringsAsFactors = F, check.names=F)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">for (j in seq(1,length(genes))){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if (genes[j] %in% tmp1$gene){<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">if (tmp1$p_val[tmp1$gene==genes[j]]<0.01){ <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> df[genes[j],i] = tmp1$avg_logFC[tmp1$gene==genes[j]]<\/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;\"> }<\/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;\">}<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">my_palette <- colorRampPalette(brewer.pal(10, \"RdBu\"))(256)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">data = data.matrix(df)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">data[data<(-1)] = -1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">data[data>1] = 1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">filename = paste0(folder,'\/avg_logFC_CAF_genes.pdf')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">pdf(filename,11,11)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\">heatmap.2(data,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> col = rev(my_palette),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> dendrogram = 'row',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> Colv= FALSE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> Rowv= TRUE,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> distfun = dist,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> hclustfun = hclust,<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> trace=\"none\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> scale = \"none\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> density.info=\"none\",<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> margins=c(5,7),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> lhei=c(1,6), lwid=c(1,4),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> keysize=0.4, key.par = list(cex=0.5),<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> cexRow=1.1,cexCol=1,srtCol=90, # rotate column label<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> key.title = 'avg_logFC',<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span style=\"font-size: 16px;\"> key.xlab = 'avg_logFC'<\/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><\/section><\/pre>\n<\/section>\n<p><br \/><\/p>\n<table style=\"width: 100%;\" width=\"-289\">\n<tbody>\n<tr>\n<td width=\"58.134216\" height=\"409.73956\" style=\"border-width: initial;border-style: none;border-color: initial;word-break: break-all;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100015205\" data-ratio=\"0.9018691588785047\" data-type=\"png\" data-w=\"428\" height=\"385 .807373046875\" width=\"427 .53985595703125\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_bia0f05fGdjGAkLoLTYIGsYuV8mPfw.png?resize=427%2C385\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcCYZWNtU5uw624JnPonDlTeGnVibia0f05fGdjGAkLoLTYIGsYuV8mPfw\/640?wx_fmt=png'\" 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;\">          <\/span><\/section>\n<table style=\"width: 100%;\">\n<tbody>\n<tr>\n<td width=\"0.0\" height=\"16.466917\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td width=\"0.0\" height=\"16.466917\" style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<\/tr>\n<tr>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\"><br \/><\/td>\n<td style=\"border-width: initial;border-style: none;border-color: initial;\">\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" data-imgfileid=\"100015209\" data-ratio=\"0.7680851063829788\" data-type=\"png\" data-w=\"470\" height=\"360.6055908203125\" width=\"469.8737487792969\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2024-01-21_\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u5206\u6790\u795e\u5668\uff013\u5206\u949f\u5e26\u4f60\u7528Seurat\u63ea\u51fa\u80bf\u7624\u201c\u81f4\u547d\u57fa\u56e0\u201d\uff01\/8_bQWKMyGSKdOvjcUyyRahrBeiaaTicA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcDUdST7Hibbk8olUQstORXDl76z7ibQWKMyGSKdOvjcUyyRahrBeiaaTicA\/640?wx_fmt=png'\" \/><span style=\"font-size: 16px;\"><br \/>\n        <\/span><\/section>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><br \/><\/p>\n<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><span style=\"font-size: 16px;font-family: "Times New Roman";letter-spacing: 0.034em;\"> <\/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;\">\u8fd9\u4e24\u5e45\u56fe\u4e2d\u7684\u7b2c\u4e00\u5e45\u56fe\u8868\u793a\u4e86\u4f17\u591a\u7684\u57fa\u56e0\u4e0e\u56db\u4e2a\u6837\u672c\u4e2d\u7684\u4e0d\u540c\u533a\u57df\u7684\u5dee\u5f02\u6027\uff0c\u53ef\u4ee5\u53d1\u73b0\u6709\u5f88\u591a\u8868\u8fbe\u5e76\u4e0d\u5177\u6709\u660e\u663e\u7684\u5dee\u5f02\u6027\u7684\u57fa\u56e0\uff0c\u56e0\u6b64\u6211\u4eec\u9700\u8981\u5728\u6b64\u57fa\u7840\u4e4b\u4e0a\u8fdb\u884c\u9009\u62e9\uff0c\u5c06\u6700\u5177\u6709\u8868\u8fbe\u5dee\u5f02\u6027\u7684\u57fa\u56e0\u6311\u9009\u51fa\u6765\uff0c\u4e8e\u662f\u5c31\u6709\u4e86\u7b2c\u4e8c\u5e45\u56fe\uff0c\u4ece\u56fe\u4e2d\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0cCOL1A1\u5728\u56db\u4e2a\u6837\u672c\u4e4b\u95f4\u7684\u5dee\u5f02\u6027\u6700\u5927\uff0c\u56fe\u4e2d\u5de6\u4e0a\u89d2\u7684\u5443\u989c\u8272\u6761\u5e26\u8868\u660e\uff0c\u989c\u8272\u8d8a\u7ea2\uff0c\u6b63\u503c\u8d8a\u5927\uff0c\u5728\u524d\u4e00\u7ec4\u7684\u8868\u8fbe\u8d8a\u660e\u663e\uff0c\u989c\u8272\u8d8a\u84dd\uff0c\u8d1f\u503c\u8d8a\u5927\uff0c\u5728\u540e\u4e00\u7ec4\u7684\u8868\u8fbe\u8d8a\u660e\u663e\uff0c\u53ef\u4ee5\u770b\u5230COL1A1\u8fd9\u4e2a\u57fa\u56e0\u7684\u5dee\u5f02\u6027\u8fd8\u662f\u975e\u5e38\u7684\u5927\u7684\u3002<\/span>    <span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">       <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/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\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u4eca\u5929\u6211\u4eec\u5229\u7528Seurat\u5305\u4ee5\u53ca\u4e00\u4e9b\u76f8\u5173\u7684\u62d3\u5c55\u5305\u5b8c\u6210\u4e86\u521d\u6b65\u7684\u80bf\u7624\u5dee\u5f02\u5316\u5206\u6790\uff0c\u4e3b\u8981\u662f\u5bf9\u7279\u5b9a\u80bf\u7624\u7684\u57fa\u56e0\u5dee\u5f02\u8fdb\u884c\u4e86\u5206\u6790\uff0c\u4ece\u800c\u627e\u5230\u4e86\u5728\u80bf\u7624\u7c07\u4e2d\u5177\u6709\u8f83\u9ad8\u8868\u7684\u7684\u57fa\u56e0\uff0c\u8fd9\u5bf9\u4e8e\u540e\u7eed\u7684\u9776\u5411\u5206\u6790\u662f\u975e\u5e38\u91cd\u8981\u7684\u3002<\/span><span style=\"font-family: \u7b49\u7ebf;letter-spacing: 0.034em;\">         <\/span><\/span><o:p style=\"font-family: \u7b49\u7ebf;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><span style=\"font-size: 16px;\"> <\/span><\/o:p><\/section>\n<section style=\"margin-left: 0pt;font-size: 10.5pt;font-family: \u7b49\u7ebf;font-weight: normal;text-align: left;text-indent: 0pt;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\u679c\u5c0f\u4f19\u4f34\u4eec\u5728\u7ed8\u56fe\u7684\u8fc7\u7a0b\u4e2d\u6709\u4efb\u4f55\u7591\u95ee\uff0c<\/span><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;color: rgb(255, 0, 0);\">\u53ef\u4ee5\u8bd5\u4e00\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u4ee5\u53ca\u6307\u4ee4\u5c31\u53ef\u4ee5\u76f4\u63a5\u7ed8\u5236\u60f3\u8981\u7684\u56fe\u5462\uff0c\u94fe\u63a5\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/span><\/section>\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<section style=\"margin-top: 8px;margin-bottom: 0px;line-height: 1.6em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100015213\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"900\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_VmRkv7tSNKliafDnsuFR7BoeDgBrww-1.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxPqeNQsFjm2HibIuSld9Nh9GicQSWhJwHjia5tEevQvDIebLErVmRkv7tSNKliafDnsuFR7BoeDgBrww\/640?wx_fmt=jpeg&from=appmsg'\" data-recalc-dims=\"1\" \/><br \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section 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, 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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\" 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