{"id":24291,"date":"2024-01-11T17:02:33","date_gmt":"2024-01-11T09:02:33","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24291"},"modified":"2024-01-11T17:02:35","modified_gmt":"2024-01-11T09:02:35","slug":"%e4%b8%80%e7%bd%91%e6%89%93%e5%b0%bd%ef%bc%81pca%ef%bc%8cumap%e5%92%8ctsne%e4%b8%89%e7%a7%8d%e9%99%8d%e7%bb%b4%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24291","title":{"rendered":"\u4e00\u7f51\u6253\u5c3d\uff01PCA\uff0cUMAP\u548ctSNE\u4e09\u79cd\u964d\u7ef4\u5206\u6790"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u60f3\u5229\u7528PCA\uff0cUMAP\u548ctSNE\u4e09\u79cd\u7b97\u6cd5\u5bf9\u540c\u4e00\u6570\u636e\u8fdb\u884c\u964d\u7ef4\u5206\u6790\uff0c\u6765\u6bd4\u8f83\u4e00\u4e0b\u4e09\u79cd\u65b9\u6cd5\u7684\u964d\u7ef4\u6548\u679c\uff0c\u5c0f\u679c\u5c06\u901a\u8fc7\u8be5\u63a8\u6587\u4e3a\u5c0f\u4f19\u4f34\u4eec\u6f14\u793a\u5982\u4f55\u5229\u7528\u8fd9\u4e09\u79cd\u5206\u6790\u65b9\u6cd5\u8fdb\u884c\u964d\u7ef4\u5206\u6790\uff0c<\/p>\n

\u6709\u9700\u8981\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ddf\u7740\u5c0f\u679c\u7684\u6b65\u4f10\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u5965\uff01<\/p>\n

    \n
  1. \u4f55\u4e3aPCA\uff0cUMAP\u548ctSNE\u5206\u6790\uff1f<\/li>\n<\/ol>\n

    PCA\u662f\u6700\u5e38\u7528\u7684\u7ebf\u6027\u964d\u7ef4\u65b9\u6cd5\uff0c\u901a\u8fc7\u67d0\u79cd\u7ebf\u6027\u6295\u5f71\uff0c\u5c06\u9ad8\u7ef4\u6570\u636e\u6620\u5c04\u5230\u4f4e\u7ef4\u7684\u7a7a\u95f4\u4e2d\u8868\u793a\uff0c\u5e76\u671f\u671b\u5728\u6240\u6295\u5f71\u7684\u7ef4\u5ea6\u4e0a\u6570\u636e\u7684\u65b9\u5dee\u6700\u5927\uff0c\u4ee5\u6b64\u4f7f\u7528\u8f83\u5c11\u7684\u6570\u636e\u7ef4\u5ea6\uff0c\u540c\u65f6\u4fdd\u7559\u4f4f\u8f83\u591a\u7684\u539f\u6570\u636e\u70b9\u7684\u7279\u6027\u3002t-SNE\u662f\u4e00\u79cd\u975e\u7ebf\u6027\u964d\u7ef4\u7b97\u6cd5\uff0c\u975e\u5e38\u9002\u7528\u4e8e\u9ad8\u7ef4\u6570\u636e\u964d\u7ef4\u52302\u7ef4\u6216\u80053\u7ef4\uff0c\u8fdb\u884c\u53ef\u89c6\u5316\uff0ct-SNE\u5177\u6709\u4e24\u5927\u4f18\u52bf\uff0c\u5bf9\u4e8e\u4e0d\u76f8\u4f3c\u7684\u70b9\uff0c\u7528\u4e00\u4e2a\u8f83\u5c0f\u7684\u8ddd\u79bb\u4f1a\u4ea7\u751f\u8f83\u5927\u7684\u68af\u5ea6\u6765\u8ba9\u8fd9\u4e9b\u70b9\u6392\u65a5\u5f00\u6765\uff0c\u8fd9\u79cd\u6392\u65a5\u53c8\u4e0d\u4f1a\u65e0\u9650\u5927\uff0c\u907f\u514d\u4e0d\u76f8\u4f3c\u7684\u70b9\u8ddd\u79bb\u592a\u8fdc\u3002UMAP\u53ef\u4ee5\u7528\u4e8e\u7c7b\u4f3c\u4e8et-SNE\u7684\u53ef\u89c6\u5316\uff0c\u4f46\u4e5f\u53ef\u4ee5\u7528\u4e8e\u4e00\u822c\u7684\u975e\u7ebf\u6027\u964d\u7ef4,\u4ee5\u4e0a\u5185\u5bb9\u5c31\u662f\u5c0f\u679c\u5bf9\u8fd9\u4e09\u79cd\u7b97\u6cd5\u539f\u7406\u7684\u7b80\u5355\u4ecb\u7ecd\uff0c\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/p>\n

    2.\u5b89\u88c5\u6240\u9700\u8981\u7684R \u5305<\/p>\n

    install.packages(\u201ctidyverse\u201d)<\/p>\n

    install.packages(\u201cbroom\u201d)<\/p>\n

    install.packages(\u201cumap\u201d)<\/p>\n

    install.packages(\u201cRtsne\u201d)<\/p>\n

    install.packages(\u201cggplot2\u201d)<\/p>\n

    3.\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/p>\n

    library(tidyverse)<\/p>\n

    library(broom)<\/p>\n

    library(umap)<\/p>\n

    library(Rtsne)<\/p>\n

    library(ggplot2)<\/p>\n

      \n
    1. \u8bfb\u53d6\u6570\u636e<\/li>\n<\/ol>\n

      #\u6570\u636e\u7c7b\u578b\u5305\u62ec\u5b57\u7b26\u4e32\u7c7b\u578b\u548c\u6570\u503c\u578b\u7c7b\u578b\u3002<\/p>\n

      df<-read.table(\u201ctest.txt\u201d,header=T)<\/p>\n

      \"Dingtalk_20230216155700\"<\/p>\n

      5.#PCA\u964d\u7ef4\u5206\u6790<\/p>\n

      penguins <- df %>%<\/p>\n

      drop_na() %>% #\u5220\u9664\u7f3a\u5931\u503c<\/p>\n

      select(-year) #\u5220\u9664year\u8fd9\u4e00\u5217\u6570\u636e<\/p>\n

      #\u4f7f\u7528prcomp()\u8fdb\u884cPCA<\/p>\n

      #PCA\u524d\u5bf9\u6570\u503c\u578b\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/p>\n

      pca_fit <- penguins %>%<\/p>\n

      select(where(is.numeric)) %>% #\u9009\u62e9\u6570\u503c\u578b\u6570\u636e<\/p>\n

      scale() %>% #\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/p>\n

      prcomp() #prcomp\u51fd\u6570\u8fdb\u884cPCA\u5206\u6790<\/p>\n

      summary(pca_fit) #\u5bf9PCA\u5206\u6790\u7ed3\u679c\u8fdb\u884c\u7edf\u8ba1<\/p>\n

      pca_fit %>%<\/p>\n

      augment(penguins) %>%<\/p>\n

      rename_at(vars(starts_with(“.fitted”)),<\/p>\n

      list(~str_replace(.,”.fitted”,””))) %>%<\/p>\n

      ggplot(aes(x=PC1,<\/p>\n

      y=PC2,<\/p>\n

      color=species,<\/p>\n

      shape=sex))+<\/p>\n

      geom_point()+<\/p>\n

      labs(x = “PC1”,<\/p>\n

      y = “PC2”)<\/p>\n

      #\u4fdd\u5b58\u56fe\u7247<\/p>\n

      ggsave(“pca.pdf”)<\/p>\n

      \"Dingtalk_20230216155048\"<\/p>\n

      6.#UMAP\u964d\u7ef4\u5206\u6790<\/p>\n

      library(umap)<\/p>\n

      theme_set(theme_bw(18))<\/p>\n

      penguins <- df%>%<\/p>\n

      drop_na() %>% #\u53bb\u9664\u7a7a\u503c<\/p>\n

      select(-year)%>% #\u5220\u9664year\u5217<\/p>\n

      mutate(ID=row_number()) #\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/p>\n

      penguins_meta <- penguins %>%<\/p>\n

      select(ID, species, island, sex) #\u7b5b\u9009\u8fd9\u4e09\u5217\u4fe1\u606f<\/p>\n

      set.seed(142)<\/p>\n

      umap_fit <- penguins %>%<\/p>\n

      select(where(is.numeric)) %>% #\u9009\u62e9\u6570\u503c\u578b\u5217\u6570\u636e<\/p>\n

      column_to_rownames(“ID”) %>% #\u5c06\u5217\u540d\u8f6c\u5316\u4e3a\u884c\u540d<\/p>\n

      scale() %>% #\u5c06\u6570\u636e\u6807\u51c6\u5316<\/p>\n

      umap()<\/p>\n

      #\u63d0\u53d6UMAP\u964d\u7ef4\u6570\u636e<\/p>\n

      umap_df <- umap_fit$layout %>%<\/p>\n

      as.data.frame()%>% #\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/p>\n

      rename(UMAP1=”V1″,#\u4fee\u6539\u5217\u540d<\/p>\n

      UMAP2=”V2″) %>%<\/p>\n

      mutate(ID=row_number())%>% #\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/p>\n

      inner_join(penguins_meta, by=”ID”) #\u5c06\u4e24\u4e2a\u6570\u636e\u8fdb\u884c\u5185\u8fde\u63a5<\/p>\n

      umap_df %>% head()<\/p>\n

      #\u7ed8\u5236UMAP\u964d\u7ef4\u6563\u70b9\u56fe<\/p>\n

      umap_df %>%<\/p>\n

      ggplot(aes(x = UMAP1,<\/p>\n

      y = UMAP2,<\/p>\n

      color = species,<\/p>\n

      shape = sex))+<\/p>\n

      geom_point()+<\/p>\n

      labs(x = “UMAP1”,<\/p>\n

      y = “UMAP2”,<\/p>\n

      subtitle = “UMAP plot”)<\/p>\n

      ggsave(“uma.pdf”)<\/p>\n

      \"Dingtalk_20230216155357\"<\/p>\n

      7.#tSNE\u964d\u7ef4\u5206\u6790<\/p>\n

      library(Rtsne)<\/p>\n

      theme_set(theme_bw(18))<\/p>\n

      penguins <- df %>%<\/p>\n

      drop_na() %>%<\/p>\n

      select(-year)%>%<\/p>\n

      mutate(ID=row_number())<\/p>\n

      penguins_meta <- penguins %>%<\/p>\n

      select(ID,species,island,sex)<\/p>\n

      set.seed(142)<\/p>\n

      tSNE_fit <- penguins %>%<\/p>\n

      select(where(is.numeric)) %>%#\u7b5b\u9009\u6570\u636e\u7c7b\u578b\u662f\u6570\u503c\u578b\u7684\u5217<\/p>\n

      column_to_rownames(“ID”) %>% #\u5c06\u5217ID\u6570\u636e\u8f6c\u6362\u4e3a\u884c\u540d<\/p>\n

      scale() %>% #\u6570\u636e\u6807\u51c6\u5316<\/p>\n

      Rtsne() #\u8fdb\u884ctSNE\u5206\u6790<\/p>\n

      #\u63d0\u53d6tSNE\u964d\u7ef4\u6570\u636e<\/p>\n

      tSNE_df <- tSNE_fit$Y %>%<\/p>\n

      as.data.frame() %>% #\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/p>\n

      rename(tSNE1=”V1″,<\/p>\n

      tSNE2=”V2″) %>% #\u4fee\u6539\u5217\u540d<\/p>\n

      mutate(ID=row_number()) #\u6dfb\u52a0\u65b0\u7684\u4e00\u5217<\/p>\n

      tSNE_df <- tSNE_df %>%<\/p>\n

      inner_join(penguins_meta, by=”ID”) #\u5185\u8fde\u63a5\uff0c\u53d6\u5171\u6709\u7684\u6570\u636e<\/p>\n

      tSNE_df %>% head()<\/p>\n

      #\u7ed8\u5236tSNE\u964d\u7ef4\u6563\u70b9\u56fe<\/p>\n

      tSNE_df %>%<\/p>\n

      ggplot(aes(x = tSNE1,<\/p>\n

      y = tSNE2,<\/p>\n

      color = species,<\/p>\n

      shape = sex))+<\/p>\n

      geom_point()+<\/p>\n

      theme(legend.position=”right”)<\/p>\n

      ggsave(“tSNE.pdf”)<\/p>\n

      \"Dingtalk_20230216155608\"<\/p>\n

      \u6700\u7ec8\u5c0f\u679c\u5229\u7528\u4e09\u79cd\u7b97\u6cd5\u8fdb\u884c\u4e86\u964d\u7ef4\u5206\u6790\uff0c\u4e0d\u540c\u7b97\u6cd5\u4ea7\u751f\u7684\u6548\u679c\u4e5f\u4e0d\u4e00\u81f4\u3002\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1ahttp:\/\/www.biocloudservice.com\/home.html,\u5305\u62ec\u4e86\u7ed8\u5236\u5355\u7ec6\u80detSNE\u56fe(http:\/\/www.biocloudservice.com\/229\/229.php),pca\u56fe\u7ed8\u5236(http:\/\/www.biocloudservice.com\/443\/443.php)\u7b49\u5c0f\u5de5\u5177\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u671f\u5f85\u548c\u5927\u5bb6\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u54c8\uff01\uff01\uff01\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

      \u4eca\u5929\u5c0f\u679c\u60f3\u5229\u7528PCA\uff0cUMAP\u548ctSNE\u4e09\u79cd\u7b97\u6cd5\u5bf9\u540c\u4e00\u6570\u636e\u8fdb\u884c\u964d\u7ef4\u5206\u6790\uff0c\u6765\u6bd4\u8f83\u4e00\u4e0b\u4e09\u79cd\u65b9\u6cd5\u7684\u964d\u7ef4\u6548\u679c\uff0c\u5c0f\u679c\u5c06\u901a […]<\/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\/24291"}],"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=24291"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24291\/revisions"}],"predecessor-version":[{"id":24296,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24291\/revisions\/24296"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24291"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24291"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24291"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}