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\/><\/p>\n<p>\u6709\u9700\u8981\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ddf\u7740\u5c0f\u82b1\u7684\u6b65\u4f10\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u55f7\uff01<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>1.\u4f55\u4e3aPCA\uff0cUMAP\u548ctSNE\u5206\u6790\uff1f<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>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\u82b1\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>2.\u5b89\u88c5\u6240\u9700\u8981\u7684R \u5305<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">install.packages(\u201ctidyverse\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cbroom\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cumap\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cRtsne\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cggplot2\u201d)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>3.\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(broom)<\/span><\/code><code><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><code><span class=\"code-snippet_outer\">library(Rtsne)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>4.\u8bfb\u53d6\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/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\">#\u6570\u636e\u7c7b\u578b\u5305\u62ec\u5b57\u7b26\u4e32\u7c7b\u578b\u548c\u6570\u503c\u578b\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df<-read.table(\u201ctest.txt\u201d,header=<span class=\"code-snippet__built_in\">T<\/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=\"0.375\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_cG6B845uzPPyU791CnpPgxaK2wlImw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGOiaXd4G2Fuh6ozVpiadUpIm7JPcG6B845uzPPyU791CnpPgxaK2wlImw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>5.#PCA\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">penguins <- df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>% <span class=\"code-snippet__comment\">#\u5220\u9664\u7f3a\u5931\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">select(-year) <span class=\"code-snippet__comment\">#\u5220\u9664year\u8fd9\u4e00\u5217\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528prcomp()\u8fdb\u884cPCA<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#PCA\u524d\u5bf9\u6570\u503c\u578b\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pca_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>% <span class=\"code-snippet__comment\">#\u9009\u62e9\u6570\u503c\u578b\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">prcomp() <span class=\"code-snippet__comment\">#prcomp\u51fd\u6570\u8fdb\u884cPCA\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">summary(pca_fit) <span class=\"code-snippet__comment\">#\u5bf9PCA\u5206\u6790\u7ed3\u679c\u8fdb\u884c\u7edf\u8ba1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pca_fit %>%<\/span><\/code><code><span class=\"code-snippet_outer\">augment(penguins) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">rename_at(vars(starts_with(<span class=\"code-snippet__string\">\".fitted\"<\/span>)),<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">list<\/span>(~str_replace(.,<span class=\"code-snippet__string\">\".fitted\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>))) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x=PC1,<\/span><\/code><code><span class=\"code-snippet_outer\">y=PC2,<\/span><\/code><code><span class=\"code-snippet_outer\">color=species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape=sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">labs(x = <span class=\"code-snippet__string\">\"PC1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">y = <span class=\"code-snippet__string\">\"PC2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4fdd\u5b58\u56fe\u7247<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"pca.pdf\"<\/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=\"0.9310793237971391\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_pBdWIyvT64KTxlCRZfzztRebhDp1XQ.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGekUj8gx5GE2hGbDaTcQkqkXYpBdWIyvT64KTxlCRZfzztRebhDp1XQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"769\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>6.#UMAP\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><code><span class=\"code-snippet_outer\">theme_set(theme_bw(<span class=\"code-snippet__number\">18<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">penguins <- df%>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>% <span class=\"code-snippet__comment\">#\u53bb\u9664\u7a7a\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">select(-year)%>% <span class=\"code-snippet__comment\">#\u5220\u9664year\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number()) <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">penguins_meta <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(ID, species, island, sex) <span class=\"code-snippet__comment\">#\u7b5b\u9009\u8fd9\u4e09\u5217\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(<span class=\"code-snippet__number\">142<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">umap_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>% <span class=\"code-snippet__comment\">#\u9009\u62e9\u6570\u503c\u578b\u5217\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">column_to_rownames(<span class=\"code-snippet__string\">\"ID\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u5c06\u5217\u540d\u8f6c\u5316\u4e3a\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u63d0\u53d6UMAP\u964d\u7ef4\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df <- umap_fit$layout %>%<\/span><\/code><code><span class=\"code-snippet_outer\">as.data.frame()%>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rename(UMAP1=<span class=\"code-snippet__string\">\"V1\"<\/span>,<span class=\"code-snippet__comment\">#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">UMAP2=<span class=\"code-snippet__string\">\"V2\"<\/span>) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number())%>% <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">inner_join(penguins_meta, by=<span class=\"code-snippet__string\">\"ID\"<\/span>) <span class=\"code-snippet__comment\">#\u5c06\u4e24\u4e2a\u6570\u636e\u8fdb\u884c\u5185\u8fde\u63a5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236UMAP\u964d\u7ef4\u6563\u70b9\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x = UMAP1,<\/span><\/code><code><span class=\"code-snippet_outer\">y = UMAP2,<\/span><\/code><code><span class=\"code-snippet_outer\">color = species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape = sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">labs(x = <span class=\"code-snippet__string\">\"UMAP1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">y = <span class=\"code-snippet__string\">\"UMAP2\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">subtitle = <span class=\"code-snippet__string\">\"UMAP plot\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"uma.pdf\"<\/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=\"0.9784656796769852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ECAZ6BLjAK0Wlm1hj0od3DicDX5TEw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGNibcv8EfyknYOcOecInqaVeoAicECAZ6BLjAK0Wlm1hj0od3DicDX5TEw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"743\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>7.#tSNE\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(Rtsne)<\/span><\/code><code><span class=\"code-snippet_outer\">theme_set(theme_bw(<span class=\"code-snippet__number\">18<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">penguins <- df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(-year)%>%<\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number())<\/span><\/code><code><span class=\"code-snippet_outer\">penguins_meta <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(ID,species,island,sex)<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(<span class=\"code-snippet__number\">142<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>%<span class=\"code-snippet__comment\">#\u7b5b\u9009\u6570\u636e\u7c7b\u578b\u662f\u6570\u503c\u578b\u7684\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">column_to_rownames(<span class=\"code-snippet__string\">\"ID\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u5c06\u5217ID\u6570\u636e\u8f6c\u6362\u4e3a\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u6570\u636e\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Rtsne() <span class=\"code-snippet__comment\">#\u8fdb\u884ctSNE\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u63d0\u53d6tSNE\u964d\u7ef4\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df <- tSNE_fit$Y %>%<\/span><\/code><code><span class=\"code-snippet_outer\">as.data.frame() %>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rename(tSNE1=<span class=\"code-snippet__string\">\"V1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">tSNE2=<span class=\"code-snippet__string\">\"V2\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number()) <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u4e00\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df <- tSNE_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">inner_join(penguins_meta, by=<span class=\"code-snippet__string\">\"ID\"<\/span>) <span class=\"code-snippet__comment\">#\u5185\u8fde\u63a5\uff0c\u53d6\u5171\u6709\u7684\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236tSNE\u964d\u7ef4\u6563\u70b9\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x = tSNE1,<\/span><\/code><code><span class=\"code-snippet_outer\">y = tSNE2,<\/span><\/code><code><span class=\"code-snippet_outer\">color = species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape = sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">theme(legend.position=<span class=\"code-snippet__string\">\"right\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"tSNE.pdf\"<\/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=\"0.9632152588555858\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_8XJlqCGvGpibwVGf174g6g9sJEkYDA.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGGA54Ln2nxbJSIVj0DAesHkOJ18XJlqCGvGpibwVGf174g6g9sJEkYDA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"734\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\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;width: 98%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;border-style: solid;border-width: 2px;border-color: rgb(160, 160, 160);padding: 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{"id":59468,"date":"2024-06-17T08:06:47","date_gmt":"2024-06-17T00:06:47","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59468"},"modified":"2024-06-17T08:06:47","modified_gmt":"2024-06-17T00:06:47","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%90-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59468","title":{"rendered":"\u4e00\u7f51\u6253\u5c3d\uff01PCA\uff0cUMAP\u548ctSNE\u4e09\u79cd\u964d\u7ef4\u5206\u6790"},"content":{"rendered":"

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center;\">\n<section style=\"width: 100%;height: 5px;background-color: rgb(255, 255, 255);\"><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>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u4eca\u5929\u5c0f\u82b1\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\u82b1\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<br \/><\/p>\n<p>\u6709\u9700\u8981\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ddf\u7740\u5c0f\u82b1\u7684\u6b65\u4f10\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u55f7\uff01<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>1.\u4f55\u4e3aPCA\uff0cUMAP\u548ctSNE\u5206\u6790\uff1f<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>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\u82b1\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>2.\u5b89\u88c5\u6240\u9700\u8981\u7684R \u5305<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">install.packages(\u201ctidyverse\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cbroom\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cumap\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cRtsne\u201d)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(\u201cggplot2\u201d)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>3.\u52a0\u8f7d\u9700\u8981\u7684R\u5305<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(broom)<\/span><\/code><code><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><code><span class=\"code-snippet_outer\">library(Rtsne)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>4.\u8bfb\u53d6\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/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\">#\u6570\u636e\u7c7b\u578b\u5305\u62ec\u5b57\u7b26\u4e32\u7c7b\u578b\u548c\u6570\u503c\u578b\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">df<-read.table(\u201ctest.txt\u201d,header=<span class=\"code-snippet__built_in\">T<\/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=\"0.375\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_cG6B845uzPPyU791CnpPgxaK2wlImw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGOiaXd4G2Fuh6ozVpiadUpIm7JPcG6B845uzPPyU791CnpPgxaK2wlImw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>5.#PCA\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">penguins <- df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>% <span class=\"code-snippet__comment\">#\u5220\u9664\u7f3a\u5931\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">select(-year) <span class=\"code-snippet__comment\">#\u5220\u9664year\u8fd9\u4e00\u5217\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528prcomp()\u8fdb\u884cPCA<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#PCA\u524d\u5bf9\u6570\u503c\u578b\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pca_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>% <span class=\"code-snippet__comment\">#\u9009\u62e9\u6570\u503c\u578b\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">prcomp() <span class=\"code-snippet__comment\">#prcomp\u51fd\u6570\u8fdb\u884cPCA\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">summary(pca_fit) <span class=\"code-snippet__comment\">#\u5bf9PCA\u5206\u6790\u7ed3\u679c\u8fdb\u884c\u7edf\u8ba1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">pca_fit %>%<\/span><\/code><code><span class=\"code-snippet_outer\">augment(penguins) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">rename_at(vars(starts_with(<span class=\"code-snippet__string\">\".fitted\"<\/span>)),<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">list<\/span>(~str_replace(.,<span class=\"code-snippet__string\">\".fitted\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>))) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x=PC1,<\/span><\/code><code><span class=\"code-snippet_outer\">y=PC2,<\/span><\/code><code><span class=\"code-snippet_outer\">color=species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape=sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">labs(x = <span class=\"code-snippet__string\">\"PC1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">y = <span class=\"code-snippet__string\">\"PC2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4fdd\u5b58\u56fe\u7247<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"pca.pdf\"<\/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=\"0.9310793237971391\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_pBdWIyvT64KTxlCRZfzztRebhDp1XQ.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGekUj8gx5GE2hGbDaTcQkqkXYpBdWIyvT64KTxlCRZfzztRebhDp1XQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"769\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>6.#UMAP\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><code><span class=\"code-snippet_outer\">theme_set(theme_bw(<span class=\"code-snippet__number\">18<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">penguins <- df%>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>% <span class=\"code-snippet__comment\">#\u53bb\u9664\u7a7a\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">select(-year)%>% <span class=\"code-snippet__comment\">#\u5220\u9664year\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number()) <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">penguins_meta <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(ID, species, island, sex) <span class=\"code-snippet__comment\">#\u7b5b\u9009\u8fd9\u4e09\u5217\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(<span class=\"code-snippet__number\">142<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">umap_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>% <span class=\"code-snippet__comment\">#\u9009\u62e9\u6570\u503c\u578b\u5217\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">column_to_rownames(<span class=\"code-snippet__string\">\"ID\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u5c06\u5217\u540d\u8f6c\u5316\u4e3a\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u63d0\u53d6UMAP\u964d\u7ef4\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df <- umap_fit$layout %>%<\/span><\/code><code><span class=\"code-snippet_outer\">as.data.frame()%>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rename(UMAP1=<span class=\"code-snippet__string\">\"V1\"<\/span>,<span class=\"code-snippet__comment\">#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">UMAP2=<span class=\"code-snippet__string\">\"V2\"<\/span>) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number())%>% <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">inner_join(penguins_meta, by=<span class=\"code-snippet__string\">\"ID\"<\/span>) <span class=\"code-snippet__comment\">#\u5c06\u4e24\u4e2a\u6570\u636e\u8fdb\u884c\u5185\u8fde\u63a5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236UMAP\u964d\u7ef4\u6563\u70b9\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">umap_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x = UMAP1,<\/span><\/code><code><span class=\"code-snippet_outer\">y = UMAP2,<\/span><\/code><code><span class=\"code-snippet_outer\">color = species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape = sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">labs(x = <span class=\"code-snippet__string\">\"UMAP1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">y = <span class=\"code-snippet__string\">\"UMAP2\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">subtitle = <span class=\"code-snippet__string\">\"UMAP plot\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"uma.pdf\"<\/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=\"0.9784656796769852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_ECAZ6BLjAK0Wlm1hj0od3DicDX5TEw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGNibcv8EfyknYOcOecInqaVeoAicECAZ6BLjAK0Wlm1hj0od3DicDX5TEw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"743\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;transform: translate3d(-15px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: center;\"><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: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(129, 167, 211);padding: 13px;\">\n<section style=\"text-align: justify;color: rgb(19, 53, 102);font-size: 16px;padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><strong>7.#tSNE\u964d\u7ef4\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">library(Rtsne)<\/span><\/code><code><span class=\"code-snippet_outer\">theme_set(theme_bw(<span class=\"code-snippet__number\">18<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">penguins <- df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">drop_na() %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(-year)%>%<\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number())<\/span><\/code><code><span class=\"code-snippet_outer\">penguins_meta <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(ID,species,island,sex)<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(<span class=\"code-snippet__number\">142<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_fit <- penguins %>%<\/span><\/code><code><span class=\"code-snippet_outer\">select(where(<span class=\"code-snippet__built_in\">is.numeric<\/span>)) %>%<span class=\"code-snippet__comment\">#\u7b5b\u9009\u6570\u636e\u7c7b\u578b\u662f\u6570\u503c\u578b\u7684\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">column_to_rownames(<span class=\"code-snippet__string\">\"ID\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u5c06\u5217ID\u6570\u636e\u8f6c\u6362\u4e3a\u884c\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">scale() %>% <span class=\"code-snippet__comment\">#\u6570\u636e\u6807\u51c6\u5316<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">Rtsne() <span class=\"code-snippet__comment\">#\u8fdb\u884ctSNE\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u63d0\u53d6tSNE\u964d\u7ef4\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df <- tSNE_fit$Y %>%<\/span><\/code><code><span class=\"code-snippet_outer\">as.data.frame() %>% <span class=\"code-snippet__comment\">#\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rename(tSNE1=<span class=\"code-snippet__string\">\"V1\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">tSNE2=<span class=\"code-snippet__string\">\"V2\"<\/span>) %>% <span class=\"code-snippet__comment\">#\u4fee\u6539\u5217\u540d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mutate(ID=row_number()) <span class=\"code-snippet__comment\">#\u6dfb\u52a0\u65b0\u7684\u4e00\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df <- tSNE_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">inner_join(penguins_meta, by=<span class=\"code-snippet__string\">\"ID\"<\/span>) <span class=\"code-snippet__comment\">#\u5185\u8fde\u63a5\uff0c\u53d6\u5171\u6709\u7684\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df %>% head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ed8\u5236tSNE\u964d\u7ef4\u6563\u70b9\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tSNE_df %>%<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(aes(x = tSNE1,<\/span><\/code><code><span class=\"code-snippet_outer\">y = tSNE2,<\/span><\/code><code><span class=\"code-snippet_outer\">color = species,<\/span><\/code><code><span class=\"code-snippet_outer\">shape = sex))+<\/span><\/code><code><span class=\"code-snippet_outer\">geom_point()+<\/span><\/code><code><span class=\"code-snippet_outer\">theme(legend.position=<span class=\"code-snippet__string\">\"right\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">ggsave(<span class=\"code-snippet__string\">\"tSNE.pdf\"<\/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=\"0.9632152588555858\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_8XJlqCGvGpibwVGf174g6g9sJEkYDA.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSY6wbcG48NZiboRfd6MhJTSGGA54Ln2nxbJSIVj0DAesHkOJ18XJlqCGvGpibwVGf174g6g9sJEkYDA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"734\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\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;width: 98%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;border-style: solid;border-width: 2px;border-color: rgb(160, 160, 160);padding: 27px;\">\n<section style=\"text-align: justify;line-height: 1.6;letter-spacing: 0px;padding-right: 6px;padding-left: 6px;\" powered-by=\"xiumi.us\">\n<p>\u6700\u7ec8\u5c0f\u82b1\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<\/p>\n<p><br \/><\/p>\n<p>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n<p><br 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