{"id":26003,"date":"2024-01-24T17:01:42","date_gmt":"2024-01-24T09:01:42","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26003"},"modified":"2024-01-24T17:01:44","modified_gmt":"2024-01-24T09:01:44","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%e5%b8%a6%e4%bd%a0%e5%bf%ab%e9%80%9f%e4%bd%bf%e7%94%a8r%e8%af%ad%e8%a8%80%e5%8c%85proxy%e5%a4%84%e7%90%86%e6%95%b0%e6%8d%ae%e9%97%b4%e7%9a%84%e8%b7%9d%e7%a6%bb%e4%bf%a1","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26003","title":{"rendered":"\u4e24\u5206\u949f\u5e26\u4f60\u5feb\u901f\u4f7f\u7528R\u8bed\u8a00\u5305proxy\u5904\u7406\u6570\u636e\u95f4\u7684\u8ddd\u79bb\u4fe1\u606f\u5e76\u8fdb\u884c\u751f\u7269\u5b66\u7814\u7a76"},"content":{"rendered":"

R\u8bed\u8a00\u662f\u4e00\u79cd\u5e7f\u6cdb\u5e94\u7528\u4e8e\u6570\u636e\u5206\u6790\u548c\u7edf\u8ba1\u5efa\u6a21\u7684\u7f16\u7a0b\u8bed\u8a00\uff0c\u5176\u751f\u6001\u7cfb\u7edf\u62e5\u6709\u4e30\u5bcc\u7684\u6269\u5c55\u5305\uff08packages\uff09\uff0c\u4ee5\u6ee1\u8db3\u5404\u79cd\u6570\u636e\u5904\u7406\u548c\u53ef\u89c6\u5316\u7684\u9700\u6c42\u3002\u201cproxy\u201d\u8bed\u8a00\u5305\u610f\u5473\u7740\u8be5\u5305\u7684\u6838\u5fc3\u76ee\u6807\u662f\u5904\u7406\u6570\u636e\u5bf9\u8c61\u4e4b\u95f4\u7684\u76f8\u4f3c\u5ea6\u6216\u8ddd\u79bb\u3002\u5728\u6570\u636e\u5206\u6790\u548c\u673a\u5668\u5b66\u4e60\u9886\u57df\uff0c\u5ea6\u91cf\u6570\u636e\u5bf9\u8c61\u4e4b\u95f4\u7684\u8ddd\u79bb\u6216\u76f8\u4f3c\u5ea6\u662f\u4e00\u4e2a\u5e38\u89c1\u800c\u91cd\u8981\u7684\u4efb\u52a1\u3002\u201cproxy\u201d\u5305\u63d0\u4f9b\u4e86\u591a\u79cd\u8ba1\u7b97\u5bf9\u8c61\u76f8\u4f3c\u6027\u7684\u65b9\u6cd5\uff0c\u5e2e\u52a9\u6570\u636e\u79d1\u5b66\u5bb6\u548c\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u5904\u7406\u6570\u636e\u3002<\/p>\n

\u8be5\u5305\u7684\u4e3b\u8981\u7279\u70b9\u4e4b\u4e00\u662f\u5176\u9ad8\u5ea6\u7684\u7075\u6d3b\u6027\u3002\u201cproxy\u201d\u5305\u4e3a\u7528\u6237\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u8ddd\u79bb\u8ba1\u7b97\u65b9\u6cd5\u548c\u76f8\u4f3c\u6027\u5ea6\u91cf\u6307\u6807\uff0c\u6db5\u76d6\u4e86\u591a\u79cd\u6570\u636e\u7c7b\u578b\u548c\u5e94\u7528\u573a\u666f\u3002\u7528\u6237\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u7814\u7a76\u9700\u6c42\u548c\u6570\u636e\u7279\u70b9\uff0c\u9009\u62e9\u5408\u9002\u7684\u8ddd\u79bb\u5ea6\u91cf\u65b9\u6cd5\u3002<\/p>\n

\u8981\u4f7f\u7528proxy\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“proxy”) #\u5b89\u88c5proxy\u8bed\u8a00\u5305<\/p>\n

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

\u5728\u5904\u7406\u5927\u89c4\u6a21\u6570\u636e\u65f6\uff0c\u8ba1\u7b97\u8ddd\u79bb\u548c\u76f8\u4f3c\u6027\u53ef\u80fd\u6210\u4e3a\u6027\u80fd\u74f6\u9888\u3002\u201cproxy\u201d\u5305\u901a\u8fc7\u4f18\u5316\u7b97\u6cd5\u548c\u5e76\u884c\u8ba1\u7b97\uff0c\u63d0\u4f9b\u4e86\u9ad8\u6548\u7684\u6570\u636e\u5904\u7406\u80fd\u529b\uff0c\u80fd\u591f\u5728\u8f83\u77ed\u7684\u65f6\u95f4\u5185\u5904\u7406\u5927\u91cf\u6570\u636e\u5bf9\u8c61\u3002<\/p>\n

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

\u6211\u4eec\u5b89\u88c5\u5e76\u52a0\u8f7d\u4e86”proxy”\u5305\uff0c\u5e76\u4f7f\u7528\u4e00\u4e2a\u7b80\u5316\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u4f5c\u4e3a\u793a\u4f8b\u6570\u636e\u3002\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u662f\u4e00\u4e2a6\u884c2\u5217\u7684\u77e9\u9635\uff0c\u5176\u4e2d\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u6837\u672c\uff0c\u5143\u7d20\u8868\u793a\u57fa\u56e0\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u503c\u3002<\/p>\n

# \u5b89\u88c5\u548c\u52a0\u8f7d\u6240\u9700\u7684\u5305<\/p>\n

> install.packages(“proxy”)<\/p>\n

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

# \u793a\u4f8b\u6570\u636e\uff1a\u5047\u8bbe\u6211\u4eec\u6709\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\uff0c\u5176\u4e2d\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u6837\u672c<\/p>\n

> gene_expression <- matrix(c(1.2, 2.3, 0.8, 4.1, 3.0, 2.5,<\/p>\n

+ 0.9, 3.2, 1.5, 2.9, 3.5, 1.7), nrow = 6, ncol = 2)<\/p>\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u4f7f\u7528proxy::dist()\u51fd\u6570\u6765\u8ba1\u7b97\u8ddd\u79bb\u77e9\u9635\u3002\u8be5\u51fd\u6570\u63a5\u53d7\u4e00\u4e2a\u6570\u636e\u77e9\u9635\u4f5c\u4e3a\u8f93\u5165\uff0c\u5e76\u8fd4\u56de\u4e00\u4e2a\u8868\u793a\u6570\u636e\u5bf9\u8c61\u4e4b\u95f4\u8ddd\u79bb\u7684dist\u5bf9\u8c61\u3002\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u6211\u4eec\u8ba1\u7b97\u4e86\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u4e2d\u6837\u672c\u4e4b\u95f4\u7684\u6b27\u6c0f\u8ddd\u79bb\u3002<\/p>\n

# \u521b\u5efa\u6570\u636e\u5bf9\u8c61\uff08dist\u5bf9\u8c61\uff09\u7528\u4e8e\u8ba1\u7b97\u8ddd\u79bb\u548c\u76f8\u4f3c\u6027<\/p>\n

> data_dist <- proxy::dist(gene_expression)<\/p>\n

# \u67e5\u770b\u8ba1\u7b97\u51fa\u7684\u8ddd\u79bb\u77e9\u9635<\/p>\n

> print(data_dist)<\/p>\n

1 2 3 4 5<\/p>\n

2 2.5495098<\/p>\n

3 0.7211103 2.2671568<\/p>\n

4 3.5227830 1.8248288 3.5846897<\/p>\n

5 3.1622777 0.7615773 2.9732137 1.2529964<\/p>\n

6 1.5264338 1.5132746 1.7117243 2.0000000 1.8681542<\/p>\n

\u8fdb\u4e00\u6b65\u4f7f\u7528\u8fd9\u4e9b\u8ddd\u79bb\u4fe1\u606f\u8fdb\u884c\u805a\u7c7b\u5206\u6790\u3001\u6837\u672c\u76f8\u4f3c\u6027\u805a\u7c7b\u3001\u591a\u7ef4\u7f29\u653e\uff08MDS\uff09\u7b49\u4efb\u52a1\uff0c\u8fd9\u4e9b\u4efb\u52a1\u901a\u5e38\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n

# \u5c42\u6b21\u805a\u7c7b<\/p>\n

> hc <- hclust(data_dist)<\/p>\n

> plot(hc)<\/p>\n

#K\u5747\u503c\u805a\u7c7b<\/p>\n

> kmeans_result <- kmeans(gene_expression, centers = 3)<\/p>\n

> cluster_labels <- kmeans_result$cluster<\/p>\n

\"755594b5-fa80-462a-a662-f3ba6cc8ca2f\"<\/p>\n

\u6837\u672c\u76f8\u4f3c\u6027\u805a\u7c7b\u662f\u5c06\u6837\u672c\u6309\u7167\u5176\u76f8\u4f3c\u6027\u8fdb\u884c\u5206\u7ec4\u7684\u8fc7\u7a0b\u3002\u53ef\u4ee5\u4f7f\u7528\u805a\u7c7b\u7b97\u6cd5\u5c06\u6837\u672c\u5206\u6210\u76f8\u4f3c\u7684\u7fa4\u7ec4\uff0c\u5e76\u8fdb\u4e00\u6b65\u5206\u6790\u6bcf\u4e2a\u7fa4\u7ec4\u7684\u7279\u5f81\u3002<\/p>\n

# \u6837\u672c\u76f8\u4f3c\u6027\u805a\u7c7b<\/p>\n

> sample_hc <- hclust(t(data_dist)) # \u4f7f\u7528\u8f6c\u7f6e\u7684\u8ddd\u79bb\u77e9\u9635\u8fdb\u884c\u6837\u672c\u805a\u7c7b<\/p>\n

> plot(sample_hc)<\/p>\n

\"09d5ab84-a6c7-416c-8a4b-66a388d57044\"<\/p>\n

\u591a\u7ef4\u7f29\u653e\uff08MDS\uff09\u662f\u4e00\u79cd\u5c06\u9ad8\u7ef4\u6570\u636e\u6620\u5c04\u5230\u4f4e\u7ef4\u7a7a\u95f4\u4ee5\u4fdd\u6301\u6837\u672c\u4e4b\u95f4\u7684\u8ddd\u79bb\u4fe1\u606f\u7684\u6280\u672f\u3002\u901a\u8fc7MDS\uff0c\u6211\u4eec\u53ef\u4ee5\u5c06\u9ad8\u7ef4\u6570\u636e\u53ef\u89c6\u5316\u4e3a\u4e8c\u7ef4\u6216\u4e09\u7ef4\u56fe\u5f62\uff0c\u66f4\u597d\u5730\u7406\u89e3\u6570\u636e\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u548c\u5dee\u5f02\u6027\u3002<\/p>\n

# \u591a\u7ef4\u7f29\u653e<\/p>\n

> mds_result <- cmdscale(data_dist, k = 2) # \u5c06\u8ddd\u79bb\u77e9\u9635\u6620\u5c04\u52302\u7ef4\u7a7a\u95f4<\/p>\n

> plot(mds_result, type = “n”)<\/p>\n

> text(mds_result, labels = rownames(gene_expression))<\/p>\n

\"f48ddee4-cc9c-49ba-bdf5-2dc8b99cc54a\"<\/p>\n

\"mds-MDS-1\"<\/p>\n

\u6b64\u5916\uff0c\u201cproxy\u201d\u5305\u8fd8\u4e0eR\u751f\u6001\u7cfb\u7edf\u4e2d\u7684\u5176\u4ed6\u5305\u7d27\u5bc6\u96c6\u6210\uff0c\u4e3a\u7528\u6237\u63d0\u4f9b\u5168\u9762\u7684\u6570\u636e\u5206\u6790\u89e3\u51b3\u65b9\u6848\u3002\u65e0\u8bba\u662f\u6570\u636e\u9884\u5904\u7406\u3001\u805a\u7c7b\u5206\u6790\u8fd8\u662f\u5206\u7c7b\u4efb\u52a1\uff0c\u201cproxy\u201d\u5305\u90fd\u80fd\u4e0e\u5176\u4ed6\u5e38\u7528\u5305\u65e0\u7f1d\u8854\u63a5\uff0c\u4f7f\u5f97\u7528\u6237\u5728\u8fdb\u884c\u590d\u6742\u7684\u6570\u636e\u5206\u6790\u5de5\u4f5c\u65f6\u5f97\u5fc3\u5e94\u624b\u3002\u8fd9\u79cd\u96c6\u6210\u6027\u4e3aR\u7528\u6237\u63d0\u4f9b\u4e86\u66f4\u52a0\u9ad8\u6548\u548c\u4fbf\u6377\u7684\u5de5\u4f5c\u6d41\u7a0b\uff0c\u4fc3\u8fdb\u4e86\u6570\u636e\u79d1\u5b66\u548c\u7edf\u8ba1\u5efa\u6a21\u9886\u57df\u7684\u53d1\u5c55\u3002<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305\u201cproxy\u201d\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0c\u5b83\u4e3aR\u7528\u6237\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u8ddd\u79bb\u8ba1\u7b97\u65b9\u6cd5\u548c\u76f8\u4f3c\u6027\u5ea6\u91cf\u6307\u6807\uff0c\u5e2e\u52a9\u7528\u6237\u5904\u7406\u591a\u79cd\u6570\u636e\u7c7b\u578b\u548c\u89c4\u6a21\u7684\u6570\u636e\u3002\u201cproxy\u201d\u5305\u7684\u8bde\u751f\u586b\u8865\u4e86R\u8bed\u8a00\u5728\u6570\u636e\u5bf9\u8c61\u8ddd\u79bb\u8ba1\u7b97\u65b9\u9762\u7684\u7a7a\u767d\uff0c\u4e3a\u6570\u636e\u79d1\u5b66\u5bb6\u548c\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5f3a\u5927\u7684\u6570\u636e\u5206\u6790\u5de5\u5177\u3002\u968f\u7740\u6570\u636e\u79d1\u5b66\u9886\u57df\u7684\u4e0d\u65ad\u53d1\u5c55\uff0c\u201cproxy\u201d\u5305\u5fc5\u5c06\u5728\u6570\u636e\u5206\u6790\u548c\u673a\u5668\u5b66\u4e60\u7684\u7814\u7a76\u4e2d\u7ee7\u7eed\u53d1\u6325\u91cd\u8981\u4f5c\u7528\uff0c\u4e3a\u7528\u6237\u5e26\u6765\u66f4\u591a\u7684\u4fbf\u5229\u548c\u53ef\u80fd\u6027\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\uff1a<\/p>\n

    \n
  1. https:\/\/www.google.com.hk\/url?sa=i&url=https%3A%2F%2Fgenomicsclass.github.io%2Fbook%2Fpages%2Fmds.html&psig=AOvVaw2XKaZZxoyBqgChaSx1nZjD&ust=1690010769749000&source=images&cd=vfe&opi=89978449&ved=0CA4QjRxqFwoTCIjz6u6in4ADFQAAAAAdAAAAABAP<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    R\u8bed\u8a00\u662f\u4e00\u79cd\u5e7f\u6cdb\u5e94\u7528\u4e8e\u6570\u636e\u5206\u6790\u548c\u7edf\u8ba1\u5efa\u6a21\u7684\u7f16\u7a0b\u8bed\u8a00\uff0c\u5176\u751f\u6001\u7cfb\u7edf\u62e5\u6709\u4e30\u5bcc\u7684\u6269\u5c55\u5305\uff08packages\uff09\uff0c\u4ee5\u6ee1\u8db3\u5404\u79cd […]<\/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\/26003"}],"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=26003"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26003\/revisions"}],"predecessor-version":[{"id":26008,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26003\/revisions\/26008"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26003"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26003"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26003"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}