{"id":27297,"date":"2024-01-31T17:05:42","date_gmt":"2024-01-31T09:05:42","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27297"},"modified":"2024-01-31T17:05:44","modified_gmt":"2024-01-31T09:05:44","slug":"%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%a4%a7%e6%95%b0%e6%8d%ae%e5%8f%af%e8%a7%86%e5%8c%96%e5%92%8c%e5%88%86%e6%9e%90%e4%b8%ad%e7%9a%84%e4%bd%bc%e4%bd%bc%e8%80%85-r%e8%af%ad%e8%a8%80%e5%8c%85pathview","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27297","title":{"rendered":"\u57fa\u56e0\u7ec4\u5927\u6570\u636e\u53ef\u89c6\u5316\u548c\u5206\u6790\u4e2d\u7684\u4f7c\u4f7c\u8005 — R\u8bed\u8a00\u5305pathview"},"content":{"rendered":"

R\u8bed\u8a00\u5305Pathview\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u5b66\u6570\u636e\u53ef\u89c6\u5316\u548c\u5206\u6790\u7684\u5de5\u5177\uff0c\u4e3b\u8981\u7528\u4e8e\u5728\u4ee3\u8c22\u901a\u8def\u548c\u4fe1\u53f7\u901a\u8def\u7b49\u65b9\u9762\u7684\u7814\u7a76\u4e2d\u53ef\u89c6\u5316\u57fa\u56e0\u7ec4\u5b66\u6570\u636e\u3002Pathview\u901a\u8fc7\u751f\u6210\u76f4\u89c2\u7684\u56fe\u5f62\u5c55\u793a\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u5927\u89c4\u6a21\u751f\u7269\u5b66\u6570\u636e\u7684\u5185\u5728\u6a21\u5f0f\u548c\u5173\u7cfb\uff0c\u4ece\u800c\u4fc3\u8fdb\u5bf9\u751f\u7269\u5b66\u8fc7\u7a0b\u7684\u6df1\u5165\u8ba4\u8bc6\u3002<\/p>\n

\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\uff0c\u9ad8\u901a\u91cf\u6280\u672f\u5982\u57fa\u56e0\u7ec4\u6d4b\u5e8f\u548c\u86cb\u767d\u8d28\u8d28\u8c31\u7b49\u4ea7\u751f\u4e86\u5927\u91cf\u7684\u6570\u636e\uff0c\u8fd9\u4e9b\u6570\u636e\u901a\u5e38\u5305\u542b\u7740\u590d\u6742\u7684\u4fe1\u606f\u3002Pathview\u7684\u6838\u5fc3\u529f\u80fd\u4e4b\u4e00\u662f\u5c06\u8fd9\u4e9b\u6570\u636e\u4e0e\u751f\u7269\u901a\u8def\u56fe\u96c6\u6210\uff0c\u4ece\u800c\u63ed\u793a\u4e0d\u540c\u901a\u8def\u4e2d\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u7684\u53d8\u5316\u60c5\u51b5\u3002\u8fd9\u79cd\u96c6\u6210\u80fd\u591f\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u76f4\u89c2\u5730\u89c2\u5bdf\u5230\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u901a\u8def\u6d3b\u6027\u7684\u53d8\u5316\uff0c\u6709\u52a9\u4e8e\u53d1\u73b0\u4e0e\u7279\u5b9a\u751f\u7269\u5b66\u8fc7\u7a0b\u76f8\u5173\u7684\u5173\u952e\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u3002<\/p>\n

\u8981\u4f7f\u7528pathview\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“pathview”) #\u5b89\u88c5pathview\u8bed\u8a00\u5305<\/p>\n

> library(pathview) #\u52a0\u8f7d\u8bed\u8a00\u5305<\/p>\n

Pathview\u4e0d\u4ec5\u63d0\u4f9b\u4e86\u9884\u5b9a\u4e49\u7684\u901a\u8def\u56fe\uff0c\u8fd8\u652f\u6301\u7528\u6237\u4e0a\u4f20\u81ea\u5b9a\u4e49\u7684\u901a\u8def\u56fe\uff0c\u4ee5\u6ee1\u8db3\u5404\u79cd\u7814\u7a76\u9700\u6c42\u3002\u7528\u6237\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u6570\u636e\u548c\u95ee\u9898\uff0c\u9009\u62e9\u5408\u9002\u7684\u901a\u8def\u56fe\u8fdb\u884c\u5206\u6790\u3002Pathview\u4f1a\u81ea\u52a8\u5c06\u57fa\u56e0\u6216\u86cb\u767d\u8d28\u7684\u8868\u8fbe\u6570\u636e\u6620\u5c04\u5230\u901a\u8def\u56fe\u4e0a\u7684\u76f8\u5e94\u4f4d\u7f6e\uff0c\u751f\u6210\u53ef\u4ea4\u4e92\u7684\u56fe\u5f62\u5c55\u793a\u3002\u8fd9\u79cd\u4ea4\u4e92\u6027\u4f7f\u7814\u7a76\u4eba\u5458\u80fd\u591f\u6df1\u5165\u63a2\u7d22\u6570\u636e\uff0c\u8fdb\u4e00\u6b65\u7406\u89e3\u57fa\u56e0\u548c\u86cb\u767d\u8d28\u5728\u901a\u8def\u4e2d\u7684\u4f5c\u7528\u548c\u76f8\u4e92\u5173\u7cfb\u3002<\/p>\n

\u793a\u4f8b\uff1a<\/p>\n

\u5047\u8bbe\u6211\u4eec\u6709\u4e00\u4e2a\u5305\u542b\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u6570\u636e\u6846gene_expression_data\uff0c\u5176\u4e2d\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u6837\u672c\u3002\u6211\u4eec\u8fd8\u6709\u4e00\u4e2a\u57fa\u56e0\u6ce8\u91ca\u6570\u636e\u6846gene_annotations\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u57fa\u56e0\u540d\u5b57\u548c\u5bf9\u5e94\u7684\u901a\u8defID\u4fe1\u606f\u3002<\/p>\n

# \u5b89\u88c5\u5e76\u52a0\u8f7d\u9700\u8981\u4f7f\u7528\u7684\u8bed\u8a00\u5305<\/p>\n

> install.packages(“pathview”)<\/p>\n

> library(pathview)<\/p>\n

# \u4f7f\u7528gene_annotations\u4e2d\u7684\u901a\u8defID\u4fe1\u606f\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca<\/p>\n

> pathway_annotations <- gene_annotations$PathwayID<\/p>\n

# \u8fd0\u884cpathview\u51fd\u6570\u8fdb\u884c\u53ef\u89c6\u5316<\/p>\n

> pathview(gene.data = gene_expression_data,<\/p>\n

+ pathway.id = pathway_annotations,<\/p>\n

+ species = “hsa”, # \u7269\u79cd\u4ee3\u7801\uff0c\u8fd9\u91cc\u4ee5\u4eba\u7c7b\u4e3a\u4f8b<\/p>\n

+ limit = list(gene = 10), # \u9650\u5236\u6bcf\u4e2a\u901a\u8def\u4e2d\u663e\u793a\u7684\u57fa\u56e0\u6570\u91cf<\/p>\n

+ kegg.native = TRUE) # \u4f7f\u7528\u539f\u751fKEGG\u56fe\u8fdb\u884c\u53ef\u89c6\u5316<\/p>\n

# \u751f\u6210\u53ef\u89c6\u5316\u56fe\u8868<\/p>\n

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

\u8fd9\u6bb5\u4ee3\u7801\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e0e\u901a\u8defID\u4fe1\u606f\u7ed3\u5408\u8d77\u6765\uff0c\u7136\u540e\u4f7f\u7528Pathview\u751f\u6210\u53ef\u4ea4\u4e92\u7684\u4ee3\u8c22\u901a\u8def\u56fe\u3002\u4f60\u53ef\u4ee5\u5728\u56fe\u8868\u4e2d\u770b\u5230\u6bcf\u4e2a\u901a\u8def\u4e2d\u57fa\u56e0\u7684\u8868\u8fbe\u6c34\u5e73\uff0c\u4e0d\u540c\u989c\u8272\u8868\u793a\u4e0d\u540c\u7684\u8868\u8fbe\u6c34\u5e73\u3002\u6b64\u5916\uff0c\u56fe\u8868\u8fd8\u63d0\u4f9b\u4e86\u4ea4\u4e92\u5f0f\u529f\u80fd\uff0c\u5141\u8bb8\u4f60\u8fdb\u4e00\u6b65\u63a2\u7d22\u57fa\u56e0\u5728\u901a\u8def\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n

\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0c\u4f60\u53ef\u4ee5\u4ece\u751f\u6210\u7684\u56fe\u8868\u4e2d\u83b7\u5f97\u6709\u5173\u57fa\u56e0\u5728\u4ee3\u8c22\u901a\u8def\u4e2d\u8868\u8fbe\u7684\u4fe1\u606f\u3002\u4f60\u8fd8\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8fdb\u884c\u8c03\u6574\uff0c\u4f8b\u5982\u4fee\u6539\u9650\u5236\u7684\u57fa\u56e0\u6570\u91cf\uff0c\u9009\u62e9\u4e0d\u540c\u7684\u7269\u79cd\u7b49\u3002<\/p>\n

\u9664\u4e86\u57fa\u672c\u7684\u53ef\u89c6\u5316\u529f\u80fd\uff0cPathview\u8fd8\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u5206\u6790\u5de5\u5177\uff0c\u7528\u4e8e\u5bf9\u6570\u636e\u8fdb\u884c\u7edf\u8ba1\u5b66\u5206\u6790\u548c\u5dee\u5f02\u6027\u5206\u6790\u3002\u8fd9\u4e9b\u5de5\u5177\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u9274\u522b\u51fa\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u663e\u8457\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u6216\u86cb\u767d\u8d28\uff0c\u5e76\u8fdb\u4e00\u6b65\u63a2\u7a76\u5b83\u4eec\u5728\u751f\u7269\u901a\u8def\u4e2d\u7684\u529f\u80fd\u3002\u901a\u8fc7\u8fd9\u4e9b\u529f\u80fd\uff0cPathview\u4e0d\u4ec5\u53ef\u4ee5\u5728\u6570\u636e\u5c42\u9762\u4e0a\u63d0\u4f9b\u4fe1\u606f\uff0c\u8fd8\u80fd\u591f\u5e2e\u52a9\u89e3\u91ca\u8fd9\u4e9b\u4fe1\u606f\u5728\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u7684\u610f\u4e49\u3002<\/p>\n

\"ksnip-20210304-152950\"<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305pathview\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0cR\u8bed\u8a00\u5305Pathview\u662f\u4e00\u4e2a\u5f3a\u5927\u7684\u751f\u7269\u5b66\u6570\u636e\u5206\u6790\u5de5\u5177\uff0c\u901a\u8fc7\u53ef\u89c6\u5316\u548c\u5206\u6790\u751f\u7269\u901a\u8def\u4e2d\u7684\u57fa\u56e0\u7ec4\u5b66\u6570\u636e\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u590d\u6742\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u3002\u5b83\u4e3a\u751f\u7269\u5b66\u5bb6\u4eec\u63d0\u4f9b\u4e86\u4e00\u4e2a\u76f4\u89c2\u7684\u5e73\u53f0\uff0c\u7528\u4e8e\u63a2\u7d22\u57fa\u56e0\u548c\u86cb\u767d\u8d28\u5728\u901a\u8def\u4e2d\u7684\u4f5c\u7528\uff0c\u4ece\u800c\u63a8\u52a8\u751f\u547d\u79d1\u5b66\u9886\u57df\u7684\u7814\u7a76\u8fdb\u5c55\u3002\u65e0\u8bba\u662f\u63ed\u793a\u75be\u75c5\u673a\u5236\u3001\u53d1\u73b0\u65b0\u7684\u6cbb\u7597\u9776\u70b9\uff0c\u8fd8\u662f\u7406\u89e3\u7ec6\u80de\u4fe1\u53f7\u4f20\u5bfc\u7f51\u7edc\uff0cPathview\u90fd\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u6709\u529b\u7684\u652f\u6301\u3002<\/p>\n

\u5c0f\u4f19\u4f34\u4eec\uff0c\u4eca\u5929\u6709\u6ca1\u6709\u5b66\u5230\u65b0\u77e5\u8bc6\u5462\uff0c\u60f3\u8981\u7ee7\u7eed\u4e86\u89e3R\u8bed\u8a00\u5185\u5bb9\u53ef\u4ee5\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff5e\uff5e\u6216\u8005\u4e5f\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u5b98\u7f51\u4e5f\u4f1a\u6301\u7eed\u66f4\u65b0\u7684\u54e6\uff5e http:\/\/www.biocloudservice.com\/home.html<\/a><\/p>\n

References:<\/p>\n

    \n
  1. https:\/\/pathview.r-forge.r-project.org\/<\/a><\/li>\n
  2. https:\/\/www.biostars.org\/p\/494579\/<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    R\u8bed\u8a00\u5305Pathview\u662f\u4e00\u4e2a\u7528\u4e8e\u751f\u7269\u5b66\u6570\u636e\u53ef\u89c6\u5316\u548c\u5206\u6790\u7684\u5de5\u5177\uff0c\u4e3b\u8981\u7528\u4e8e\u5728\u4ee3\u8c22\u901a\u8def\u548c\u4fe1\u53f7\u901a\u8def\u7b49\u65b9\u9762\u7684\u7814\u7a76\u4e2d\u53ef\u89c6 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27297"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=27297"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27297\/revisions"}],"predecessor-version":[{"id":27304,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27297\/revisions\/27304"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27297"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27297"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27297"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}