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powered-by=\"xiumi.us\">\n<p>\u5c0f\u4f19\u4f34\u4eec\u5927\u5bb6\u597d\uff0c\u6211\u8fd8\u662f\u90a3\u4e2a\u5927\u6d77\u54e5\uff0c\u4eca\u5929\u5927\u6d77\u54e5\u8981\u5206\u4eab\u7684\u8fd8\u662f\u63a5\u7740\u524d\u51e0\u5929\u5206\u4eab\u7684GISTIC2.0\u6559\u5b66\uff0c\u4e0d\u8fc7\u4eca\u5929\u662f\u8fd9\u4e2a\u6559\u5b66\u7684\u6700\u540e\u4e00\u7bc7\uff01\u7ec8\u4e8e\u8981\u5b8c\u7ed3\u4e86\uff0c\u5e0c\u671b\u4f60\u4eec\u53ef\u4ee5\u628a\u8fd9\u4e2a\u6280\u672f\u7262\u8bb0\u4e8e\u5fc3\u54e6\uff01\u4e0d\u8bf4\u9898\u5916\u8bdd\u4e86~\u4eca\u5929\u5927\u6d77\u54e5\u8981\u7528\u5230\u4e00\u4e2aR\u5305\uff0c\u540d\u5b57\u53eb\u505amaftools\uff0c\u90a3\u4e48\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u5148\u4e86\u89e3\u4e00\u4e0b\u4ec0\u4e48\u662fmaftools\uff1f<\/p>\n<p>“maftools” 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powered-by=\"xiumi.us\">\n<p><strong>\u6570\u636e\u52a0\u8f7d\u4e0e\u5904\u7406\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>“maftools” \u5141\u8bb8\u7528\u6237\u52a0\u8f7dMAF\u6587\u4ef6\uff0c\u5e76\u5bf9\u6570\u636e\u8fdb\u884c\u5fc5\u8981\u7684\u9884\u5904\u7406\u548c\u8fc7\u6ee4\uff0c\u4ee5\u4fbf\u540e\u7eed\u5206\u6790\u3002<\/p>\n<p>\u7a81\u53d8\u9891\u7387\u5206\u6790\uff1a\u7528\u6237\u53ef\u4ee5\u4f7f\u7528”maftools” \u5305\u7ed8\u5236\u7a81\u53d8\u7684\u9891\u7387\u5206\u5e03\u76f4\u65b9\u56fe\u3001\u67f1\u72b6\u56fe\u7b49\uff0c\u5e2e\u52a9\u4ed6\u4eec\u4e86\u89e3\u6bcf\u4e2a\u57fa\u56e0\u7684\u7a81\u53d8\u9891\u7387\u548c\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u7a81\u53d8\u7c7b\u578b\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u8be5\u5305\u80fd\u591f\u7ed8\u5236\u4e0d\u540c\u7a81\u53d8\u7c7b\u578b\uff08\u4f8b\u5982\u9519\u4e49\u7a81\u53d8\u3001\u65e0\u4e49\u7a81\u53d8\u3001\u63d2\u5165\u3001\u7f3a\u5931\u7b49\uff09\u7684\u5206\u5e03\u56fe\uff0c\u4ee5\u53ca\u8fd9\u4e9b\u7a81\u53d8\u7c7b\u578b\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u57fa\u56e0\u7ea7\u522b\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u7528\u6237\u53ef\u4ee5\u901a\u8fc7”maftools” \u5305\u5728\u57fa\u56e0\u7ea7\u522b\u4e0a\u8fdb\u884c\u5206\u6790\uff0c\u5305\u62ec\u7ed8\u5236\u57fa\u56e0\u7a81\u53d8\u9891\u7387\u3001\u7a81\u53d8\u8c31\u3001\u70ed\u56fe\u7b49\uff0c\u6709\u52a9\u4e8e\u4e86\u89e3\u54ea\u4e9b\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u6700\u5e38\u89c1\u7684\u7a81\u53d8\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u751f\u5b58\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u8be5\u5305\u5141\u8bb8\u7528\u6237\u57fa\u4e8eMAF\u6570\u636e\u8fdb\u884c\u751f\u5b58\u5206\u6790\uff0c\u63a2\u7a76\u7a81\u53d8\u4e0e\u60a3\u8005\u751f\u5b58\u7387\u4e4b\u95f4\u7684\u5173\u7cfb\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u590d\u6742\u53d8\u5f02\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">“maftools” \u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u8bc6\u522b\u5e76\u7ed8\u5236\u51fa\u590d\u6742\u53d8\u5f02\u6a21\u5f0f\uff0c\u6bd4\u5982\u591a\u57fa\u56e0\u7a81\u53d8\u3001\u5408\u5e76\u7a81\u53d8\u7b49\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u7a81\u53d8\u6ce8\u91ca\u53ef\u89c6\u5316\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u7528\u6237\u53ef\u4ee5\u901a\u8fc7”maftools” \u5c06\u7a81\u53d8\u6ce8\u91ca\u4fe1\u606f\uff08\u5982\u529f\u80fd\u5f71\u54cd\u3001COSMIC\u6ce8\u91ca\u7b49\uff09\u4e0e\u7a81\u53d8\u6570\u636e\u7ed3\u5408\u5728\u4e00\u8d77\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u7a81\u53d8\u7684\u529f\u80fd\u548c\u610f\u4e49\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4e92\u4f5c\u7f51\u7edc\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u8be5\u5305\u8fd8\u652f\u6301\u6784\u5efa\u57fa\u4e8e\u7a81\u53d8\u6570\u636e\u7684\u86cb\u767d\u8d28\u4e92\u4f5c\u7f51\u7edc\uff0c\u4ee5\u63ed\u793a\u7a81\u53d8\u5728\u7ec6\u80de\u4fe1\u53f7\u901a\u8def\u4e2d\u7684\u5f71\u54cd\u3002<\/p>\n<p>\u603b\u4e4b\uff0c”maftools” \u662f\u4e00\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u90a3\u4e48\u8bf4\u4e86\u8fd9\u4e48\u591a\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<\/section>\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;vertical-align: middle;width: auto;align-self: center;flex: 100 100 0%;height: auto;\">\n<section style=\"overflow: hidden;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;\">\n<section style=\"transform: rotate(0.1deg);\">\n<section style=\"width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 100%;margin-right: -6px;margin-left: -7px;border-bottom: 2px dotted rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;padding-right: 18px;padding-left: 18px;\">\n<section style=\"text-align: center;margin-top: 20px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 13px 8px 0px;border-color: rgb(93, 91, 92) rgba(255, 255, 255, 0) rgb(251, 133, 129);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;height: auto;align-self: center;\">\n<section style=\"overflow: hidden;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;\">\n<section style=\"transform: rotate(0.1deg);\">\n<section style=\"width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 100%;margin-right: -6px;margin-left: -7px;border-bottom: 2px dotted rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u603b\u4e4b\uff0c”maftools” \u662f\u4e00\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u90a3\u4e48\u8bf4\u4e86\u8fd9\u4e48\u591a\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<p>#\u4e0a\u6b21\u6211\u4eec\u8bf4\u5230\uff0c\u901a\u8fc7\u5728\u7ebf\u5206\u6790\uff0c\u5f97\u5230\u4e86\u4e0b\u56fe\u4e2d\u7684\u4e00\u5806\u6587\u4ef6<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0408805031446542\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_lZg1w4IqkRblq0qyxENMeTcCXZfEBg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrzzrJOytIsSocGI8YX3BPt3hhlZg1w4IqkRblq0qyxENMeTcCXZfEBg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"318\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u73b0\u5728\u8ba9\u6211\u4eec\u6765\u5904\u7406\u5427!<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5efa\u8bae\u4e0b\u8f7dgithub\u6700\u65b0\u7248\u672c\u7684maftools\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(maftools)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u5165GISTIC\u8f93\u51fa\u7684\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">laml.gistic = readGistic(gisticAllLesionsFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/all_lesions.conf_99.txt'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> gisticAmpGenesFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/amp_genes.conf_99.txt'<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> gisticDelGenesFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/del_genes.conf_99.txt'<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> gisticScoresFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/scores.gistic'<\/span>, isTCGA = <span class=\"code-snippet__built_in\">T<\/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 class=\"code-snippet__comment\">#\u7136\u540e\u7a0d\u7b49\u7247\u523b\uff0c\u8fd9\u4e00\u6b65\u52a0\u8f7d\u9700\u8981\u6d88\u8017\u4e00\u4e22\u4e22\u65f6\u95f4~<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5f00\u59cb\u53ef\u89c6\u5316\u91cd\u8981\u7684\u7ed3\u679c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#genome plot \u90e8\u5206\u7a81\u51fa\u4e86\u660e\u663e\u7684\u6269\u589e\u548c\u5220\u5931\u533a\u57df<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticChromPlot(gistic = laml.gistic, ref.build = <span class=\"code-snippet__string\">'hg38'<\/span>) <span class=\"code-snippet__comment\">## \u53c2\u8003\u57fa\u56e0\u7ec4\u9009hg38<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7148148148148148\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_8wibfeNJ6AGLtxJCibsZWQuQg1ibDQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKruoj2ffGneQh51hFiawLBzUiaR0APic8wibfeNJ6AGLtxJCibsZWQuQg1ibDQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Bubble plot \u7ed8\u5236\u663e\u8457\u6539\u53d8\u7684cytobands,\u4ee5\u53ca\u6539\u53d8\u7684\u6837\u672c\u6570\u548c\u5b83\u6240\u5305\u542b\u7684\u57fa\u56e0\u6570\u7684\u51fd\u6570\u3002\u6bcf\u4e00\u4e2a\u6c14\u6ce1\u7684\u5927\u5c0f\u662f\u6839\u636e-log10\u8f6c\u5316q\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticBubblePlot(gistic = laml.gistic)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6527777777777778\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_znWz0OicfOpEeiblQxxM3A7Lbht7jw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrYw2yUjTqRzyX1kM1Xns1xGDPGwznWz0OicfOpEeiblQxxM3A7Lbht7jw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#oncoplot <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticOncoPlot(gistic = laml.gistic, <\/span><\/code><code><span class=\"code-snippet_outer\"> sortByAnnotation = <span class=\"code-snippet__literal\">TRUE<\/span>, top =<span class=\"code-snippet__number\">20<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6916666666666667\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_1m1OhC8vlBLsWCMgMVo0OGmicBxhZQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrAeicce2cibaIvD7NGxLnJOXibWJ41m1OhC8vlBLsWCMgMVo0OGmicBxhZQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u8fd8\u53ef\u4ee5\u6311\u9009\u51faq\u503c\u5c0f\u4e8e0.25\u7684\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">(sig_cytoband <- laml.gistic@cytoband.summary %>% <\/span><\/code><code><span class=\"code-snippet_outer\">filter(qvalues<<span class=\"code-snippet__number\">0.25<\/span>) %>% .$Unique_Name)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u770b\u770b\u6269\u5c55\u57fa\u56e0\u6709\u591a\u5c11<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">table(grepl(pattern = <span class=\"code-snippet__string\">\"AP\"<\/span>,sig_cytoband))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## FALSE TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## 34 3<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u6311\u9009q\u503c\u5c0f\u4e8e0.25\u7684Amplification cytoband<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_AP_cytoband <- laml.gistic@cytoband.summary %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> filter(qvalues<<span class=\"code-snippet__number\">0.25<\/span>) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> .$Unique_Name %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> .[grepl(pattern = <span class=\"code-snippet__string\">\"AP\"<\/span>,.)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06Amplification \u7684\u57fa\u56e0\u6311\u9009\u51fa\u6765<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_AP_gene <- laml.gistic@data %>% filter(Cytoband %in% sig_AP_cytoband) %>% .$Hugo_Symbol <\/span><\/code><code><span class=\"code-snippet_outer\">unique(sig_AP_gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u540c\u6837\u7684\u6311\u9009\u51fa\u4e22\u5931\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06Deletion cytoband \u7684\u57fa\u56e0\u6311\u9009\u51fa\u6765<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_gene <- laml.gistic@data %>% filter(Cytoband %in% sig_DP_cytoband) %>% .$Hugo_Symbol <\/span><\/code><code><span class=\"code-snippet_outer\">unique(sig_DP_gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u627e\u5230\u4e86\u57fa\u56e0\u4e4b\u540e\u5c31\u53ef\u4ee5\u201c\u4e3a\u6240\u6b32\u4e3a\u4e86\u2026.\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u62f7\u8d1d\u6570\u7f3a\u5931\u533a\u57df\u7684\u57fa\u56e0\u90a3\u4e48\u591a\uff0c\u6765\u4e2aGO\u3001kegg\u3001GSEA\u8fd9\u4e9b\u5206\u6790\u662f\u4e0d\u662f\u90fd\u53ef\u4ee5\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7b80\u5355\u5bcc\u96c6\u5206\u6790\u4e00\u4e0b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Hs.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(topGO)<\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_entrezId = mapIds(x = org.Hs.eg.db,<\/span><\/code><code><span class=\"code-snippet_outer\"> keys = unique(sig_DP_gene),<\/span><\/code><code><span class=\"code-snippet_outer\"> keytype = <span class=\"code-snippet__string\">\"SYMBOL\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> column = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_entrezId <- na.omit(sig_DP_entrezId)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">go_ALL <- enrichGO(gene = sig_DP_entrezId,<\/span><\/code><code><span class=\"code-snippet_outer\"> OrgDb = org.Hs.eg.db,<\/span><\/code><code><span class=\"code-snippet_outer\"> keyType = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> ont = <span class=\"code-snippet__string\">\"ALL\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalueCutoff = <span class=\"code-snippet__number\">0.5<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> qvalueCutoff = <span class=\"code-snippet__number\">0.5<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##\u5206\u6790\u5b8c\u6210\u540e\uff0c\u4f5c\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">### \u6570\u76ee\u592a\u591a\uff0c\u6211\u53ea\u8981\u5404\u4e2a\u6761\u76ee\u7684\u524d6\u4e2a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">BP_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"BP\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">CC_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"CC\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">MF_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"MF\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">go_df <- rbind(BP_df,CC_df,MF_df)<\/span><\/code><code><span class=\"code-snippet_outer\">go_df$go_term_order=factor(x = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">1<\/span>:nrow(go_df)),labels = go_df$Description)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggsci)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(data=go_df, aes(x=go_term_order,y=Count, fill=ONTOLOGY)) +<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_bar(stat=<span class=\"code-snippet__string\">\"identity\"<\/span>, width=<span class=\"code-snippet__number\">0.8<\/span>) + <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_jama() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_classic() +<\/span><\/code><code><span class=\"code-snippet_outer\"> xlab(<span class=\"code-snippet__string\">\"GO term\"<\/span>) + ylab(<span class=\"code-snippet__string\">\"Number of Genes\"<\/span>) + labs(title = <span class=\"code-snippet__string\">\"The Most Enriched GO Terms\"<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> theme(axis.text.x=element_text(face = <span class=\"code-snippet__string\">\"bold\"<\/span>, color=<span class=\"code-snippet__string\">\"gray50\"<\/span>,angle = <span class=\"code-snippet__number\">60<\/span>,vjust = <span class=\"code-snippet__number\">1<\/span>, hjust = <span class=\"code-snippet__number\">1<\/span> ))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6425925925925926\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_EVfHK44e43f7I0WGBvhOgGgTMUxrNw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrvhcwlV1IEEBSVibnIuIaibGZgCEVfHK44e43f7I0WGBvhOgGgTMUxrNw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section 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justify;\">\n<p>\u603b\u7ed3\u65f6\u95f4\u5230\uff01\u4e09\u8282\u5206\u6790\u6784\u6210\u7684\u6559\u5b66\u53ef\u4ee5\u4f53\u73b0\u51faGISTIC2.0\u7684\u5168\u90e8\u5206\u6790\u6d41\u7a0b\u4e4b\u591a\uff0c\u4f46\u662f\u4e5f\u8bf4\u660e\u4e86\u8fd9\u4e2a\u5206\u6790\u662f\u503c\u5f97\u5927\u5bb6\u5b66\u4e60\u7684\uff0c\u4e5f\u5e0c\u671b\u5927\u5bb6\u53ef\u4ee5\u81ea\u5df1\u52a8\u624b\u8bd5\u8bd5\u54e6\uff01\u6bd5\u7adf\u7ec6\u8282\u5f88\u591a\uff0c\u5f88\u591a\u5176\u4e2d\u7684\u73af\u8282\u90fd\u9700\u8981\u4eb2\u81ea\u52a8\u624b\u624d\u80fd\u9886\u609f\u54e6\uff01<\/p>\n<p>\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2<\/p>\n<p><span style=\"letter-spacing: 0px;\">\u7f51\u5740 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powered-by=\"xiumi.us\">\n<p>\u5c0f\u4f19\u4f34\u4eec\u5927\u5bb6\u597d\uff0c\u6211\u8fd8\u662f\u90a3\u4e2a\u5927\u6d77\u54e5\uff0c\u4eca\u5929\u5927\u6d77\u54e5\u8981\u5206\u4eab\u7684\u8fd8\u662f\u63a5\u7740\u524d\u51e0\u5929\u5206\u4eab\u7684GISTIC2.0\u6559\u5b66\uff0c\u4e0d\u8fc7\u4eca\u5929\u662f\u8fd9\u4e2a\u6559\u5b66\u7684\u6700\u540e\u4e00\u7bc7\uff01\u7ec8\u4e8e\u8981\u5b8c\u7ed3\u4e86\uff0c\u5e0c\u671b\u4f60\u4eec\u53ef\u4ee5\u628a\u8fd9\u4e2a\u6280\u672f\u7262\u8bb0\u4e8e\u5fc3\u54e6\uff01\u4e0d\u8bf4\u9898\u5916\u8bdd\u4e86~\u4eca\u5929\u5927\u6d77\u54e5\u8981\u7528\u5230\u4e00\u4e2aR\u5305\uff0c\u540d\u5b57\u53eb\u505amaftools\uff0c\u90a3\u4e48\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u5148\u4e86\u89e3\u4e00\u4e0b\u4ec0\u4e48\u662fmaftools\uff1f<\/p>\n<p>“maftools” \u5305\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u7528\u4e8e\u5206\u6790\u548c\u5c55\u793aMAF\u6587\u4ef6\u4e2d\u7a81\u53d8\u6570\u636e\u7684\u529f\u80fd\uff0c\u4f7f\u7814\u7a76\u4eba\u5458\u80fd\u591f\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u80bf\u7624\u4e2d\u7684\u9057\u4f20\u53d8\u5f02\u3002<\/p>\n<p><strong>\u4ee5\u4e0b\u662f\u4e00\u4e9b”maftools” \u5305\u63d0\u4f9b\u7684\u4e3b\u8981\u529f\u80fd\uff1a<\/strong><\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u6570\u636e\u52a0\u8f7d\u4e0e\u5904\u7406\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>“maftools” \u5141\u8bb8\u7528\u6237\u52a0\u8f7dMAF\u6587\u4ef6\uff0c\u5e76\u5bf9\u6570\u636e\u8fdb\u884c\u5fc5\u8981\u7684\u9884\u5904\u7406\u548c\u8fc7\u6ee4\uff0c\u4ee5\u4fbf\u540e\u7eed\u5206\u6790\u3002<\/p>\n<p>\u7a81\u53d8\u9891\u7387\u5206\u6790\uff1a\u7528\u6237\u53ef\u4ee5\u4f7f\u7528”maftools” \u5305\u7ed8\u5236\u7a81\u53d8\u7684\u9891\u7387\u5206\u5e03\u76f4\u65b9\u56fe\u3001\u67f1\u72b6\u56fe\u7b49\uff0c\u5e2e\u52a9\u4ed6\u4eec\u4e86\u89e3\u6bcf\u4e2a\u57fa\u56e0\u7684\u7a81\u53d8\u9891\u7387\u548c\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u7a81\u53d8\u7c7b\u578b\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u8be5\u5305\u80fd\u591f\u7ed8\u5236\u4e0d\u540c\u7a81\u53d8\u7c7b\u578b\uff08\u4f8b\u5982\u9519\u4e49\u7a81\u53d8\u3001\u65e0\u4e49\u7a81\u53d8\u3001\u63d2\u5165\u3001\u7f3a\u5931\u7b49\uff09\u7684\u5206\u5e03\u56fe\uff0c\u4ee5\u53ca\u8fd9\u4e9b\u7a81\u53d8\u7c7b\u578b\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u57fa\u56e0\u7ea7\u522b\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u7528\u6237\u53ef\u4ee5\u901a\u8fc7”maftools” \u5305\u5728\u57fa\u56e0\u7ea7\u522b\u4e0a\u8fdb\u884c\u5206\u6790\uff0c\u5305\u62ec\u7ed8\u5236\u57fa\u56e0\u7a81\u53d8\u9891\u7387\u3001\u7a81\u53d8\u8c31\u3001\u70ed\u56fe\u7b49\uff0c\u6709\u52a9\u4e8e\u4e86\u89e3\u54ea\u4e9b\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u6700\u5e38\u89c1\u7684\u7a81\u53d8\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u751f\u5b58\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u8be5\u5305\u5141\u8bb8\u7528\u6237\u57fa\u4e8eMAF\u6570\u636e\u8fdb\u884c\u751f\u5b58\u5206\u6790\uff0c\u63a2\u7a76\u7a81\u53d8\u4e0e\u60a3\u8005\u751f\u5b58\u7387\u4e4b\u95f4\u7684\u5173\u7cfb\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u590d\u6742\u53d8\u5f02\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">“maftools” \u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u8bc6\u522b\u5e76\u7ed8\u5236\u51fa\u590d\u6742\u53d8\u5f02\u6a21\u5f0f\uff0c\u6bd4\u5982\u591a\u57fa\u56e0\u7a81\u53d8\u3001\u5408\u5e76\u7a81\u53d8\u7b49\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u7a81\u53d8\u6ce8\u91ca\u53ef\u89c6\u5316\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u7528\u6237\u53ef\u4ee5\u901a\u8fc7”maftools” \u5c06\u7a81\u53d8\u6ce8\u91ca\u4fe1\u606f\uff08\u5982\u529f\u80fd\u5f71\u54cd\u3001COSMIC\u6ce8\u91ca\u7b49\uff09\u4e0e\u7a81\u53d8\u6570\u636e\u7ed3\u5408\u5728\u4e00\u8d77\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u7a81\u53d8\u7684\u529f\u80fd\u548c\u610f\u4e49\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding-right: 20px;padding-left: 20px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4e92\u4f5c\u7f51\u7edc\u5206\u6790\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u8be5\u5305\u8fd8\u652f\u6301\u6784\u5efa\u57fa\u4e8e\u7a81\u53d8\u6570\u636e\u7684\u86cb\u767d\u8d28\u4e92\u4f5c\u7f51\u7edc\uff0c\u4ee5\u63ed\u793a\u7a81\u53d8\u5728\u7ec6\u80de\u4fe1\u53f7\u901a\u8def\u4e2d\u7684\u5f71\u54cd\u3002<\/p>\n<p>\u603b\u4e4b\uff0c”maftools” \u662f\u4e00\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u90a3\u4e48\u8bf4\u4e86\u8fd9\u4e48\u591a\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<\/section>\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;vertical-align: middle;width: auto;align-self: center;flex: 100 100 0%;height: auto;\">\n<section style=\"overflow: hidden;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;\">\n<section style=\"transform: rotate(0.1deg);\">\n<section style=\"width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 100%;margin-right: -6px;margin-left: -7px;border-bottom: 2px dotted rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;padding-right: 18px;padding-left: 18px;\">\n<section style=\"text-align: center;margin-top: 20px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 13px 8px 0px;border-color: rgb(93, 91, 92) rgba(255, 255, 255, 0) rgb(251, 133, 129);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;height: auto;align-self: center;\">\n<section style=\"overflow: hidden;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;\">\n<section style=\"transform: rotate(0.1deg);\">\n<section style=\"width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 100%;margin-right: -6px;margin-left: -7px;border-bottom: 2px dotted rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 6px;height: 6px;border-radius: 100%;background-color: rgb(93, 91, 92);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u603b\u4e4b\uff0c”maftools” \u662f\u4e00\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u90a3\u4e48\u8bf4\u4e86\u8fd9\u4e48\u591a\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01<\/p>\n<p>#\u4e0a\u6b21\u6211\u4eec\u8bf4\u5230\uff0c\u901a\u8fc7\u5728\u7ebf\u5206\u6790\uff0c\u5f97\u5230\u4e86\u4e0b\u56fe\u4e2d\u7684\u4e00\u5806\u6587\u4ef6<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0408805031446542\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_lZg1w4IqkRblq0qyxENMeTcCXZfEBg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrzzrJOytIsSocGI8YX3BPt3hhlZg1w4IqkRblq0qyxENMeTcCXZfEBg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"318\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u73b0\u5728\u8ba9\u6211\u4eec\u6765\u5904\u7406\u5427!<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5efa\u8bae\u4e0b\u8f7dgithub\u6700\u65b0\u7248\u672c\u7684maftools\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(maftools)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u5165GISTIC\u8f93\u51fa\u7684\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">laml.gistic = readGistic(gisticAllLesionsFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/all_lesions.conf_99.txt'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> gisticAmpGenesFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/amp_genes.conf_99.txt'<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> gisticDelGenesFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/del_genes.conf_99.txt'<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> gisticScoresFile = <span class=\"code-snippet__string\">'.\/Gistic 2.0 results\/scores.gistic'<\/span>, isTCGA = <span class=\"code-snippet__built_in\">T<\/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 class=\"code-snippet__comment\">#\u7136\u540e\u7a0d\u7b49\u7247\u523b\uff0c\u8fd9\u4e00\u6b65\u52a0\u8f7d\u9700\u8981\u6d88\u8017\u4e00\u4e22\u4e22\u65f6\u95f4~<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5f00\u59cb\u53ef\u89c6\u5316\u91cd\u8981\u7684\u7ed3\u679c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#genome plot \u90e8\u5206\u7a81\u51fa\u4e86\u660e\u663e\u7684\u6269\u589e\u548c\u5220\u5931\u533a\u57df<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticChromPlot(gistic = laml.gistic, ref.build = <span class=\"code-snippet__string\">'hg38'<\/span>) <span class=\"code-snippet__comment\">## \u53c2\u8003\u57fa\u56e0\u7ec4\u9009hg38<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7148148148148148\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_8wibfeNJ6AGLtxJCibsZWQuQg1ibDQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKruoj2ffGneQh51hFiawLBzUiaR0APic8wibfeNJ6AGLtxJCibsZWQuQg1ibDQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Bubble plot \u7ed8\u5236\u663e\u8457\u6539\u53d8\u7684cytobands,\u4ee5\u53ca\u6539\u53d8\u7684\u6837\u672c\u6570\u548c\u5b83\u6240\u5305\u542b\u7684\u57fa\u56e0\u6570\u7684\u51fd\u6570\u3002\u6bcf\u4e00\u4e2a\u6c14\u6ce1\u7684\u5927\u5c0f\u662f\u6839\u636e-log10\u8f6c\u5316q\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticBubblePlot(gistic = laml.gistic)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6527777777777778\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_znWz0OicfOpEeiblQxxM3A7Lbht7jw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrYw2yUjTqRzyX1kM1Xns1xGDPGwznWz0OicfOpEeiblQxxM3A7Lbht7jw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#oncoplot <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gisticOncoPlot(gistic = laml.gistic, <\/span><\/code><code><span class=\"code-snippet_outer\"> sortByAnnotation = <span class=\"code-snippet__literal\">TRUE<\/span>, top =<span class=\"code-snippet__number\">20<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6916666666666667\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_1m1OhC8vlBLsWCMgMVo0OGmicBxhZQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrAeicce2cibaIvD7NGxLnJOXibWJ41m1OhC8vlBLsWCMgMVo0OGmicBxhZQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u8fd8\u53ef\u4ee5\u6311\u9009\u51faq\u503c\u5c0f\u4e8e0.25\u7684\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">(sig_cytoband <- laml.gistic@cytoband.summary %>% <\/span><\/code><code><span class=\"code-snippet_outer\">filter(qvalues<<span class=\"code-snippet__number\">0.25<\/span>) %>% .$Unique_Name)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u770b\u770b\u6269\u5c55\u57fa\u56e0\u6709\u591a\u5c11<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">table(grepl(pattern = <span class=\"code-snippet__string\">\"AP\"<\/span>,sig_cytoband))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## FALSE TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## 34 3<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u6311\u9009q\u503c\u5c0f\u4e8e0.25\u7684Amplification cytoband<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_AP_cytoband <- laml.gistic@cytoband.summary %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> filter(qvalues<<span class=\"code-snippet__number\">0.25<\/span>) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> .$Unique_Name %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> .[grepl(pattern = <span class=\"code-snippet__string\">\"AP\"<\/span>,.)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06Amplification \u7684\u57fa\u56e0\u6311\u9009\u51fa\u6765<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_AP_gene <- laml.gistic@data %>% filter(Cytoband %in% sig_AP_cytoband) %>% .$Hugo_Symbol <\/span><\/code><code><span class=\"code-snippet_outer\">unique(sig_AP_gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u540c\u6837\u7684\u6311\u9009\u51fa\u4e22\u5931\u57fa\u56e0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06Deletion cytoband \u7684\u57fa\u56e0\u6311\u9009\u51fa\u6765<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_gene <- laml.gistic@data %>% filter(Cytoband %in% sig_DP_cytoband) %>% .$Hugo_Symbol <\/span><\/code><code><span class=\"code-snippet_outer\">unique(sig_DP_gene)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u627e\u5230\u4e86\u57fa\u56e0\u4e4b\u540e\u5c31\u53ef\u4ee5\u201c\u4e3a\u6240\u6b32\u4e3a\u4e86\u2026.\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u62f7\u8d1d\u6570\u7f3a\u5931\u533a\u57df\u7684\u57fa\u56e0\u90a3\u4e48\u591a\uff0c\u6765\u4e2aGO\u3001kegg\u3001GSEA\u8fd9\u4e9b\u5206\u6790\u662f\u4e0d\u662f\u90fd\u53ef\u4ee5\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7b80\u5355\u5bcc\u96c6\u5206\u6790\u4e00\u4e0b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Hs.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(topGO)<\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_entrezId = mapIds(x = org.Hs.eg.db,<\/span><\/code><code><span class=\"code-snippet_outer\"> keys = unique(sig_DP_gene),<\/span><\/code><code><span class=\"code-snippet_outer\"> keytype = <span class=\"code-snippet__string\">\"SYMBOL\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> column = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sig_DP_entrezId <- na.omit(sig_DP_entrezId)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">go_ALL <- enrichGO(gene = sig_DP_entrezId,<\/span><\/code><code><span class=\"code-snippet_outer\"> OrgDb = org.Hs.eg.db,<\/span><\/code><code><span class=\"code-snippet_outer\"> keyType = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> ont = <span class=\"code-snippet__string\">\"ALL\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalueCutoff = <span class=\"code-snippet__number\">0.5<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> qvalueCutoff = <span class=\"code-snippet__number\">0.5<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##\u5206\u6790\u5b8c\u6210\u540e\uff0c\u4f5c\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">### \u6570\u76ee\u592a\u591a\uff0c\u6211\u53ea\u8981\u5404\u4e2a\u6761\u76ee\u7684\u524d6\u4e2a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">BP_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"BP\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">CC_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"CC\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">MF_df<- go_ALL@result %>% arrange(desc(Count)) %>% filter(ONTOLOGY==<span class=\"code-snippet__string\">\"MF\"<\/span>) %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\">go_df <- rbind(BP_df,CC_df,MF_df)<\/span><\/code><code><span class=\"code-snippet_outer\">go_df$go_term_order=factor(x = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">1<\/span>:nrow(go_df)),labels = go_df$Description)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggsci)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(data=go_df, aes(x=go_term_order,y=Count, fill=ONTOLOGY)) +<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_bar(stat=<span class=\"code-snippet__string\">\"identity\"<\/span>, width=<span class=\"code-snippet__number\">0.8<\/span>) + <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_jama() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_classic() +<\/span><\/code><code><span class=\"code-snippet_outer\"> xlab(<span class=\"code-snippet__string\">\"GO term\"<\/span>) + ylab(<span class=\"code-snippet__string\">\"Number of Genes\"<\/span>) + labs(title = <span class=\"code-snippet__string\">\"The Most Enriched GO Terms\"<\/span>)+ <\/span><\/code><code><span class=\"code-snippet_outer\"> theme(axis.text.x=element_text(face = <span class=\"code-snippet__string\">\"bold\"<\/span>, color=<span class=\"code-snippet__string\">\"gray50\"<\/span>,angle = <span class=\"code-snippet__number\">60<\/span>,vjust = <span class=\"code-snippet__number\">1<\/span>, hjust = <span class=\"code-snippet__number\">1<\/span> ))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6425925925925926\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_EVfHK44e43f7I0WGBvhOgGgTMUxrNw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTxOr6cy9aFkWibeAKkZRwKrvhcwlV1IEEBSVibnIuIaibGZgCEVfHK44e43f7I0WGBvhOgGgTMUxrNw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;letter-spacing: 0px;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u5b8c\u7ed3\u6492\u82b1\uff01\uff01\uff01~~~\uff0c\u91cc\u9762\u7684\u7ec6\u8282\u7a0d\u5fae\u8c03\u8c03\u56fe\uff0c\u6309\u9700\u7f8e\u5316\uff0c\u5c31\u53ef\u4ee5\u653e\u6587\u7ae0\u91cc\u9762\u5566\uff01<\/span><\/p>\n<\/section>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;\">\n<section style=\"text-align: right;margin-right: 0%;margin-bottom: -20px;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 100 100 0%;align-self: flex-start;height: auto;border-right: 0px none rgb(62, 62, 62);border-top-right-radius: 12px;overflow: hidden;box-shadow: rgb(231, 215, 173) 0px 6px 0px;\">\n<section style=\"margin: 20px 0% 30px;\" powered-by=\"xiumi.us\">\n<section style=\"padding-right: 10px;padding-left: 10px;text-align: justify;\">\n<p>\u603b\u7ed3\u65f6\u95f4\u5230\uff01\u4e09\u8282\u5206\u6790\u6784\u6210\u7684\u6559\u5b66\u53ef\u4ee5\u4f53\u73b0\u51faGISTIC2.0\u7684\u5168\u90e8\u5206\u6790\u6d41\u7a0b\u4e4b\u591a\uff0c\u4f46\u662f\u4e5f\u8bf4\u660e\u4e86\u8fd9\u4e2a\u5206\u6790\u662f\u503c\u5f97\u5927\u5bb6\u5b66\u4e60\u7684\uff0c\u4e5f\u5e0c\u671b\u5927\u5bb6\u53ef\u4ee5\u81ea\u5df1\u52a8\u624b\u8bd5\u8bd5\u54e6\uff01\u6bd5\u7adf\u7ec6\u8282\u5f88\u591a\uff0c\u5f88\u591a\u5176\u4e2d\u7684\u73af\u8282\u90fd\u9700\u8981\u4eb2\u81ea\u52a8\u624b\u624d\u80fd\u9886\u609f\u54e6\uff01<\/p>\n<p>\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2<\/p>\n<p><span style=\"letter-spacing: 0px;\">\u7f51\u5740 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