{"id":25065,"date":"2024-01-18T16:40:45","date_gmt":"2024-01-18T08:40:45","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25065"},"modified":"2024-01-18T16:40:47","modified_gmt":"2024-01-18T08:40:47","slug":"%e4%b8%bb%e6%88%90%e5%88%86%e5%88%86%e6%9e%90pca%ef%bc%8c%e4%bd%a0%e4%b8%8d%e6%87%82%e7%9a%84%e9%83%bd%e5%9c%a8%e8%bf%99%e4%ba%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25065","title":{"rendered":"\u4e3b\u6210\u5206\u5206\u6790PCA\uff0c\u4f60\u4e0d\u61c2\u7684\u90fd\u5728\u8fd9\u4e86"},"content":{"rendered":"

\u8bb8\u591a\u751f\u4fe1\u5206\u6790\u62a5\u544a\u91cc\u90fd\u4f1a\u6709\u4e0a\u4e00\u5f20PCA\u56fe\uff0c\u90a3\u5b83\u662f\u4ec0\u4e48\uff0c\u53c8\u4e3a\u4ec0\u4e48\u4f1a\u5982\u6b64\u91cd\u8981\u5462\uff1f\u5c0f\u679c\u4eca\u5929\u5c31\u4e3a\u5927\u5bb6\u8bb2\u89e3\u3002<\/p>\n

\u4e3b\u6210\u5206\u5206\u6790\uff08Principal Component Analysis\uff0cPCA\uff09\u662f\u505a\u751f\u4fe1\u5206\u6790\u7684\u4e00\u79cd\u975e\u5e38\u5e38\u7528\u7684\u6570\u636e\u5206\u6790\u7b97\u6cd5\uff0c\u5b83\u5728\u505a\u9ad8\u7ef4\u6570\u636e\u5206\u6790\u65f6\u6781\u4e3a\u6709\u7528\u5e7f\u6cdb\u5e94\u7528\u4e8e\u591a\u9886\u57df\uff0c\u5982\u533b\u5b66\u7814\u7a76\u3001\u5e02\u573a\u5206\u6790\u548c\u8d22\u52a1\u5206\u6790\u7b49\u3002<\/p>\n

\u5b83\u7684\u539f\u7406\u662f\u901a\u8fc7\u5bf9\u534f\u65b9\u5dee\u77e9\u9635\u8fdb\u884c\u7279\u5f81\u5206\u89e3\uff0c\u4ee5\u5f97\u51fa\u6570\u636e\u7684\u4e3b\u6210\u5206\u4e0e\u5b83\u4eec\u7684\u6743\u503c\uff0c\u5373\u7279\u5f81\u503c\u548c\u7279\u5f81\u5411\u91cf\u3002\u5b83\u4ea7\u751f\u7684\u7ed3\u679c\u53ef\u4ee5\u7406\u89e3\u4e3a\u5bf9\u539f\u6570\u636e\u4e2d\u7684\u65b9\u5dee\u505a\u51fa\u89e3\u91ca\uff1a\u54ea\u4e00\u4e2a\u65b9\u5411\u4e0a\u7684\u6570\u636e\u503c\u5bf9\u65b9\u5dee\u7684\u5f71\u54cd\u6700\u5927\uff1f<\/p>\n

\u5c0f\u679c\u8fd9\u91cc\u4e3e\u4e2a\u6817\u5b50 ,\u6bd4\u5982\u6211\u4eec\u5f97\u5230\u4e86\u4e00\u7ec4\u8f6c\u5f55\u7ec4\u8868\u8fbe\u6570\u636e\uff0c\u5176\u4e2d\u6709n\u4e2a\u8f6c\u5f55\u672c\u7684\u8868\u8fbe\u91cf\u4fe1\u606f\u3002\u90a3\u4e48\u6211\u4eec\u5c31\u6709n\u4e2a\u53d8\u91cf\u4e86\uff0c\u8fd9\u4e2an\u6709\u65f6\u4f1a\u975e\u5e38\u5927\uff0c\u4f1a\u5230\u4e0a\u767e\u4e07\u5343\u4e07\u3002\u82e5\u662f\u76f4\u63a5\u53bb\u5bf9\u6bd4\u4e24\u4e2a\u6216\u591a\u4e2a\u6570\u636e\uff0c\u5c31\u663e\u5f97\u975e\u5e38\u56f0\u96be\u3002\u7ecf\u8fc7\u4e3b\u6210\u5206\u5206\u6790\u540e\uff0c\u5c31\u53ef\u4ee5\u5c06\u8fd9n\u4e2a\u53d8\u91cf\u964d\u7ef4\u5230r\u4e2a\u91cf(r<n)\u3002<\/p>\n

\u8fd9r\u4e2a\u4e3b\u6210\u5206\u4f1a\u4f9d\u636e\u65b9\u5dee\u7684\u5927\u5c0f\u8fdb\u884c\u6392\u5e8f\uff0c\u79f0\u4f5c\u4e3b\u6210\u5206\uff08PC\uff091\u3001\u4e3b\u6210\u52062\u3001\u2026\u2026\u4e3b\u6210\u5206r\u3002\u800c\u6bcf\u4e2a\u4e3b\u6210\u5206\u7684\u65b9\u5dee\u5728\u8fd9\u4e00\u7ec4\u53d8\u91cf\u4e2d\u7684\u603b\u65b9\u5dee\u4e2d\u6240\u5360\u7684\u6bd4\u4f8b\uff0c\u5373\u662f\u4e3b\u6210\u5206\u7684\u8d21\u732e\u5ea6\u3002\u901a\u5e38\u6765\u8bf4\uff0c\u6211\u4eec\u4ec5\u8003\u5bdf\u8d21\u732e\u5ea6\u524d2\u6216\u8005\u524d3\u7684\u4e3b\u6210\u5206\uff0c\u7ecf\u8fc7\u53ef\u89c6\u5316\u540e\uff0c\u5373\u5f97\u5230\u4e86\u4e8c\u7ef4\u6216\u4e09\u7ef4PCA\u6563\u70b9\u56fe\u3002<\/p>\n

PCA\u63d0\u4f9b\u4e86\u4e00\u79cd\u964d\u4f4e\u6570\u636e\u7ef4\u5ea6\u7684\u6709\u6548\u529e\u6cd5\uff1b\u5982\u679c\u5206\u6790\u8005\u5728\u539f\u6570\u636e\u4e2d\u9664\u6389\u6700\u5c0f\u7684\u7279\u5f81\u503c\u6240\u5bf9\u5e94\u7684\u6210\u5206\uff0c\u90a3\u4e48\u6240\u5f97\u7684\u4f4e\u7ef4\u5ea6\u6570\u636e\u5fc5\u5b9a\u662f\u6700\u4f18\u5316\u7684\uff08\u4e5f\u5373\uff0c\u8fd9\u6837\u964d\u4f4e\u7ef4\u5ea6\u5fc5\u5b9a\u662f\u5931\u53bb\u4fe1\u606f\u6700\u5c11\u7684\u65b9\u6cd5\uff09\u3002<\/p>\n

\u4e0b\u9762\u5c0f\u679c\u901a\u8fc7\u4e00\u4e2a\u6848\u4f8b\u6765\u8ba9\u5927\u5bb6\u66f4\u6df1\u5165\u5730\u5b66\u4e60\u3002<\/p>\n

\u52a0\u8f7dR\u5305\u548c\u6570\u636e<\/h1>\n

#\u52a0\u8f7dR\u5305\u548c\u6570\u636e<\/p>\n

library(tidyverse)<\/p>\n

library(“factoextra”)<\/p>\n

data(“decathlon2”)<\/p>\n

df <- decathlon2[1:23, 1:10] #\u5220\u9664\u5206\u7c7b\u53d8\u91cf<\/p>\n

\u89c2\u5bdf\u4e00\u4e0b\u6570\u636e\uff0c\u6570\u636e\u7c7b\u578b\u4e3a\u6570\u636e\u6846”data.frame”\uff0c23\u884c\uff0c10\u5217\u3002<\/p>\n

<\/p>\n

\u6570\u636e\u7684\u53d8\u91cf\u5206\u522b\u662f100\u7c73\u3001400\u7c73\u3001\u8df3\u8fdc\u3001\u94c5\u7403\u7b49\u4f53\u80b2\u9879\u76ee<\/p>\n

<\/p>\n

\u884c\u662f\u4e0d\u540c\u4eba\u7684\u540d\u5b57<\/p>\n

<\/p>\n

\u63a5\u4e0b\u6765\u6211\u4eec\u5f00\u59cb\u6b63\u5f0f\u5bf9\u8fd9\u4e2a\u6570\u636e\u96c6\u8fdb\u884c\u4e3b\u6210\u5206\u5206\u6790<\/p>\n

\u4e3b\u6210\u5206\u5206\u6790<\/h1>\n

1.\u5206\u6790<\/h2>\n

\u672c\u6b21\u6848\u4f8b\u4f7f\u7528\u7684\u662fR\u8bed\u8a00\u81ea\u5e26\u7684\u4e3b\u6210\u5206\u5206\u6790\u51fd\u6570\uff0cprcomp\u548c princomp\uff0c\u5b83\u4eec\u53ef\u4ee5\u5f88\u597d\u7684\u4e0e\u5176\u4ed6\u7684\u5305\u517c\u5bb9\u3002\u540e\u7eed\u4f1a\u7ed3\u5408factoextra\u5305\u8fdb\u884c\u6570\u636e\u7684\u53ef\u89c6\u5316\u3002<\/p>\n

#\u4e3b\u6210\u5206\u5206\u6790<\/p>\n

res.pca <- prcomp(df,scale. = T)<\/p>\n

\u901a\u8fc7\u8fd9\u6837\u4e00\u884c\u4ee3\u7801\u5c31\u53ef\u4ee5\u5bf9\u6570\u636e\u5b8c\u6210\u4e3b\u6210\u5206\u5206\u6790<\/p>\n

\u7528get_eig\uff08\uff09\u51fd\u6570\u83b7\u5f97\u5206\u6790\u7684\u7ed3\u679c\u3002<\/p>\n

<\/p>\n

\u8fd4\u56de\u7684\u4e09\u4e2a\u5217\uff0c\u5206\u522b\u662f\u7279\u5f81\u503c\uff08eigenvalue\uff09\u3001\u65b9\u5dee\u8d21\u732e\u7387\uff08variance.percent\uff09\u548c\u7d2f\u79ef\u65b9\u5dee\u8d21\u732e\u7387\uff08cumulative.variance.percent\uff09\u3002\u603b\u5171\u6709\u5341\u4e2a\u53d8\u91cf\u4e5f\u5c31\u662f10\u4e2a\u7ef4\u5ea6\u3002\u7279\u5f81\u503c\u4f9d\u6b21\u4ece\u5927\u5230\u5c0f\u6392\u5217\uff0c\u5bf9\u5e94\u7684\u65b9\u5dee\u8d21\u732e\u7387\u4e5f\u662f\u4ece\u5927\u5230\u5c0f\u6392\u5217\u7684\u8d8b\u52bf\u3002\u8fd9\u610f\u5473\u7740\u6392\u540d\u5728\u524d\u9762\u7684\u5c31\u662f\u6570\u636e\u7684\u4e3b\u6210\u5206\u3002<\/p>\n

\u6570\u636e\u7684\u65b9\u5dee\u7b49\u4e8e\u534f\u65b9\u5dee\u6240\u6709\u7279\u5f81\u503c\u4e4b\u548c\uff0c\u7b2ci\u4e2a\u4e3b\u6210\u5206\u7684\u65b9\u5dee\u7b49\u4e8e\u534f\u65b9\u5dee\u77e9\u9635\u7684\u7b2ci\u4e2a\u7279\u5f81\u503c\u3002\u7136\u540e\u4ece\u524d\u5230\u540e\u6c42\u548c\u5c31\u5f97\u5230\u7d2f\u79ef\u65b9\u5dee\u8d21\u732e\u7387<\/strong>\u3002\u6240\u4ee5\u7d2f\u79ef\u65b9\u5dee\u8d21\u732e\u7387\u7684\u5927\u5c0f\u8868\u793a\u4e86\u5f53\u524d\u9009\u62e9\u7684\u6240\u6709\u4e3b\u6210\u5206\u643a\u5e26\u539f\u6570\u636e\u7684\u4fe1\u606f\u7684\u6bd4\u4f8b\u3002<\/p>\n

\u4e00\u822c\u60c5\u51b5\u4e0b\u4f1a\u9009\u62e990%\u4e3a\u9650\uff0c\u4f46\u662f\u5c0f\u679c\u63d0\u793a\u8fd9\u91cc\u8fd8\u662f\u8981\u5177\u4f53\u60c5\u51b5\u5177\u4f53\u5206\u6790\u54e6\u3002<\/p>\n

2.\u7ed3\u679c\u53ef\u89c6\u5316<\/h2>\n

2.1 \u788e\u77f3\u56fe<\/p>\n

fviz_screeplot(res.pca, addlabels = TRUE, ylim = c(0, 45))<\/p>\n

<\/p>\n

\u53cd\u6620\u5404\u6210\u5206\u65b9\u5dee\u89e3\u91ca\u6bd4\u4f8b\uff0c\u975e\u5e38\u76f4\u89c2\u3002<\/p>\n

2.2\u7279\u5f81\u503c<\/h2>\n

fviz_screeplot(res.pca,<\/p>\n

choice=”eigenvalue”,<\/p>\n

addlabels = TRUE,<\/p>\n

ylim = c(0, 4.5))<\/p>\n

\u5341\u4e2a\u53d8\u91cf\u7684\u7279\u5f81\u503c\u6392\u5e8f<\/p>\n

<\/p>\n

2.3\u67e5\u770b\u53d8\u91cf\u7684\u5206\u5e03<\/h2>\n

<\/p>\n

# \u53d8\u91cf\u5206\u5e03\u53ef\u89c6\u5316<\/p>\n

fviz_pca_var(res.pca,<\/p>\n

col.var=”contrib”, \u00a0 # \u6839\u636e\u8d21\u732e\u5ea6\u7740\u8272<\/p>\n

gradient.cols = c(“#00AFBB”, “#E7B800”, “#FC4E07”),<\/p>\n

repel = TRUE<\/p>\n

)<\/p>\n

<\/p>\n

\u8fd9\u4e2a\u56fe\u5c0f\u679c\u6559\u4f60\u600e\u4e48\u770b\u3002<\/p>\n

\u53d8\u91cf\u8d21\u732e\u56fe\u663e\u793a\u4e86\u6bcf\u4e2a\u53d8\u91cf\u5728\u4e3b\u6210\u5206\u4e0a\u7684\u8d21\u732e\u3002\u7ebf\u6761\u8d8a\u957f\u8d8a\u63a5\u8fd1\u7ea2\u8272\uff0c\u5bf9\u5e94\u7684\u4e3b\u6210\u5206\u8d21\u732e\u8f83\u5927\u3002\u6a2a\u7eb5\u5750\u6807\u5206\u522b\u4ee3\u8868\u4e3b\u6210\u52061 \uff0c\u4e3b\u6210\u52062\uff0c\u767e\u5206\u6bd4\u662f\u4e3b\u6210\u52061 2\u7684\u65b9\u5dee\u89e3\u91ca\u3002<\/p>\n

\u5bf9Dim1\u6765\u8bf4\u8981\u6a2a\u7740\u770b\uff0c\u5bf9\u5176\u5f71\u54cd\u6700\u5927\u7684\u662f100m\u548cLong.jump\u4e24\u4e2a\u53d8\u91cf\u3002<\/p>\n

\u5bf9Dim2\u6765\u8bf4\u8981\u7ad6\u7740\u770b\uff0c\u5bf9\u5176\u5f71\u54cd\u6700\u5927\u7684\u662f1500m\u548cPole.vault\u4e24\u4e2a\u53d8\u91cf\u3002<\/p>\n

2.4\u7279\u5f81\u5bf9\u4e3b\u6210\u52061\u7684\u8d21\u732e<\/h2>\n

#\u7279\u5f81\u8d21\u732e<\/p>\n

fviz_contrib(res.pca, choice = “var”, axes = 1, top = 10)<\/p>\n

<\/p>\n

2.5\u6837\u672cPCA<\/p>\n

\u6837\u672cPCA\u5206\u5e03\uff0c\u901a\u5e38\u4e5f\u662f\u8bba\u6587\u91cc\u51fa\u73b0\u9891\u6b21\u6700\u9ad8\u7684PCA\u56fe\u3002\u5c0f\u679c\u8fd9\u91cc\u9009\u62e9\u4e86\u6709\u4e09\u7ec4\u6570\u636e\u7684\u9e22\u5c3e\u82b1\u6570\u636e\u96c6\u8fdb\u884c\u5c55\u793a\u3002<\/p>\n

#\u6837\u672cpca\u56fe<\/p>\n

iris.pca <- prcomp(iris[,-5])<\/p>\n

fviz_pca_ind(iris.pca,<\/p>\n

label = “none”, # hide individual labels<\/p>\n

habillage = iris$Species, # color by groups<\/p>\n

palette = c(“#00AFBB”, “#E7B800”, “#FC4E07”),<\/p>\n

addEllipses = TRUE # Concentration ellipses<\/p>\n

)<\/p>\n

<\/p>\n

\u901a\u8fc7\u8d21\u732e\u6700\u9ad8\u7684\u4e24\u4e2a\u4e3b\u6210\u5206\uff0c\u5728\u4e00\u4e2a\u4e8c\u7ef4\u7684\u5e73\u9762\u4e0a\uff0c\u5c31\u80fd\u5728\u56fe\u50cf\u4e0a\u663e\u793a\u8fd9\u4e9b\u6570\u636e\u7684\u4e0d\u540c\u7ec4\u3002<\/p>\n

\u597d\u60a8\u662f\u5426\u660e\u767d\u4e86\u5462\uff0c\u5982\u679c\u6709\u4e0d\u61c2\u7684\u6765\u548c\u5c0f\u679c\u8ba8\u8bba\u5427~<\/p>\n

PCA\u5206\u6790\u76f8\u5173\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1a<\/p>\n

http:\/\/www.biocloudservice.com\/home.html<\/p>\n","protected":false},"excerpt":{"rendered":"

\u8bb8\u591a\u751f\u4fe1\u5206\u6790\u62a5\u544a\u91cc\u90fd\u4f1a\u6709\u4e0a\u4e00\u5f20PCA\u56fe\uff0c\u90a3\u5b83\u662f\u4ec0\u4e48\uff0c\u53c8\u4e3a\u4ec0\u4e48\u4f1a\u5982\u6b64\u91cd\u8981\u5462\uff1f\u5c0f\u679c\u4eca\u5929\u5c31\u4e3a\u5927\u5bb6\u8bb2\u89e3\u3002 \u4e3b\u6210\u5206\u5206\u6790\uff08 […]<\/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\/25065"}],"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=25065"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25065\/revisions"}],"predecessor-version":[{"id":25076,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25065\/revisions\/25076"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25065"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25065"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25065"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}