{"id":26878,"date":"2024-01-29T17:25:37","date_gmt":"2024-01-29T09:25:37","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26878"},"modified":"2024-01-29T17:25:38","modified_gmt":"2024-01-29T09:25:38","slug":"matrixgenerics%e8%af%ad%e8%a8%80%e5%8c%85%ef%bc%8c%e7%ae%80%e5%8c%96%e6%95%b0%e6%8d%ae%ef%bc%8c%e6%9b%b4%e5%bf%ab%e7%9a%84%e6%93%8d%e4%bd%9c%e5%b9%b6%e8%ae%a1%e7%ae%97%e6%95%b0%e6%8d%ae%e7%9f%a9","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26878","title":{"rendered":"MatrixGenerics\u8bed\u8a00\u5305\uff0c\u7b80\u5316\u6570\u636e\uff0c\u66f4\u5feb\u7684\u64cd\u4f5c\u5e76\u8ba1\u7b97\u6570\u636e\u77e9\u9635\u7ed3\u6784"},"content":{"rendered":"

MatrixGenerics\u662f\u4e00\u6b3e\u5f3a\u5927\u4e14\u4e0e\u751f\u7269\u5b66\u76f8\u5173\u7684R\u8bed\u8a00\u5305\uff0c\u5b83\u662f\u7531Martin Morgan\u5728R\u8bed\u8a00\u793e\u533a\u4e2d\u5f00\u53d1\u7684\u3002Martin Morgan\u662f\u4e00\u4f4d\u8d44\u6df1\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5bb6\u548cR\u8bed\u8a00\u7a0b\u5e8f\u5458\uff0c\u4ed6\u5728R\u8bed\u8a00\u751f\u6001\u7cfb\u7edf\u4e2d\u8d21\u732e\u4e86\u8bb8\u591a\u6709\u7528\u7684\u5305\u548c\u5de5\u5177\u3002\u8be5\u5305\u7684\u8bbe\u8ba1\u5f3a\u8c03\u4e86\u4ee3\u7801\u7684\u6a21\u5757\u5316\u548c\u53ef\u6269\u5c55\u6027\uff0c\u8fd9\u4f7f\u5f97\u7528\u6237\u80fd\u591f\u66f4\u8f7b\u677e\u5730\u7f16\u5199\u53ef\u8bfb\u6027\u5f3a\u3001\u53ef\u7ef4\u62a4\u6027\u597d\u7684\u4ee3\u7801\u3002<\/p>\n

\u751f\u7269\u5b66\u9886\u57df\u7684\u6570\u636e\u901a\u5e38\u4ee5\u77e9\u9635\u6216\u6570\u7ec4\u7684\u5f62\u5f0f\u5b58\u50a8\uff0c\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3001DNA\u6d4b\u5e8f\u6570\u636e\u3001\u86cb\u767d\u8d28\u4e92\u4f5c\u7f51\u7edc\u7b49\u3002MatrixGenerics\u5305\u7684\u4e3b\u8981\u76ee\u6807\u662f\u4e3a\u8fd9\u4e9b\u590d\u6742\u7684\u6570\u636e\u7ed3\u6784\u63d0\u4f9b\u901a\u7528\u7684\u51fd\u6570\uff0c\u7b80\u5316\u751f\u7269\u5b66\u5bb6\u4eec\u5bf9\u6570\u636e\u7684\u5904\u7406\u548c\u5206\u6790\u3002\u5176\u6838\u5fc3\u529f\u80fd\u662f\u5728\u4e0d\u540c\u7c7b\u578b\u7684\u77e9\u9635\u548c\u6570\u7ec4\u4e0a\u6267\u884c\u901a\u7528\u64cd\u4f5c\uff0c\u4f8b\u5982\u8ba1\u7b97\u5747\u503c\u3001\u6c42\u548c\u3001\u6807\u51c6\u5dee\u4ee5\u53ca\u884c\u5217\u53d8\u6362\u7b49\u3002<\/p>\n

\u8981\u4f7f\u7528MatrixGenerics\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“MatrixGenerics”) #\u5b89\u88c5MatrixGenerics\u8bed\u8a00\u5305<\/p>\n

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

MatrixGenerics\u7684\u4f18\u52bf\u4e4b\u4e00\u662f\u5176\u5bf9\u5e7f\u6cdb\u7684\u77e9\u9635\u7c7b\u5bf9\u8c61\u7684\u652f\u6301\uff0c\u5305\u62ecMatrix\u5305\u4e2d\u5b9a\u4e49\u7684\u5404\u79cd\u7279\u6b8a\u77e9\u9635\u7c7b\u578b\uff0c\u5982dgCMatrix\u3001dgTMatrix\u3001dsCMatrix\u7b49\u3002\u8fd9\u4f7f\u5f97\u751f\u7269\u5b66\u5bb6\u53ef\u4ee5\u5728\u4e0d\u540c\u7684\u6570\u636e\u7c7b\u578b\u4e4b\u95f4\u65e0\u7f1d\u5207\u6362\uff0c\u5e76\u4e14\u4e0d\u5fc5\u4e3a\u6bcf\u79cd\u6570\u636e\u7c7b\u578b\u5355\u72ec\u7f16\u5199\u51fd\u6570\u3002<\/p>\n

\u6b64\u5916\uff0cMatrixGenerics\u8fd8\u652f\u6301\u7528\u6237\u81ea\u5b9a\u4e49\u77e9\u9635\u7c7b\u7684\u6269\u5c55\uff0c\u4f7f\u5176\u80fd\u591f\u9002\u5e94\u7279\u5b9a\u7684\u751f\u7269\u5b66\u6570\u636e\u9700\u6c42\u3002\u7528\u6237\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u5b9a\u4e49\u65b0\u7684\u77e9\u9635\u7c7b\uff0c\u5e76\u5728\u5176\u4e0a\u5e94\u7528MatrixGenerics\u7684\u51fd\u6570\uff0c\u4ece\u800c\u66f4\u597d\u5730\u5904\u7406\u751f\u7269\u5b66\u6570\u636e\u3002<\/p>\n

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

# \u5b89\u88c5\u548c\u52a0\u8f7dMatrixGenerics\u5305<\/p>\n

> install.packages(“MatrixGenerics”)<\/p>\n

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

# \u52a0\u8f7d\u5176\u4ed6\u5fc5\u8981\u7684\u5305<\/p>\n

> install.packages(“ggplot2”)<\/p>\n

> library(ggplot2)<\/p>\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u521b\u5efa\u4e00\u4e2a\u6a21\u62df\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u96c6\uff0c\u5e76\u5c06\u5176\u8f6c\u6362\u4e3aMatrix\u5bf9\u8c61\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528MatrixGenerics\u5305\u4e2d\u7684\u51fd\u6570\u6765\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5904\u7406\u548c\u53ef\u89c6\u5316\u3002<\/p>\n

# \u521b\u5efa\u6a21\u62df\u57fa\u56e0\u8868\u8fbe\u6570\u636e<\/p>\n

> gene_names <- c(“Gene1”, “Gene2”, “Gene3”, “Gene4”, “Gene5”)<\/p>\n

> sample_names <- c(“Sample1”, “Sample2”, “Sample3”)<\/p>\n

> expr_data <- matrix(data = rnorm(15, mean = 10, sd = 2), nrow = 5, ncol = 3, dimnames = list(gene_names, sample_names))<\/p>\n

# \u5c06\u6570\u636e\u8f6c\u6362\u4e3aMatrix\u5bf9\u8c61<\/p>\n

> expr_data_matrix <- as(expr_data, “matrix”)<\/p>\n

> # \u8ba1\u7b97\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u503c<\/p>\n

> gene_means <- rowMeans(expr_data_matrix)<\/p>\n

# \u53ef\u89c6\u5316\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u503c<\/p>\n

> gene_means_plot <- ggplot(data.frame(gene = gene_names, mean_expr = gene_means), aes(x = gene, y = mean_expr)) +<\/p>\n

+ geom_bar(stat = “identity”) +<\/p>\n

+ labs(title = “Average Gene Expression”,<\/p>\n

+ x = “Gene”,<\/p>\n

+ y = “Mean Expression”)<\/p>\n

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

\"c29b4a06-3d7f-4f19-ac7f-89648de91094\"<\/p>\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u8ba1\u7b97\u6bcf\u4e2a\u6837\u672c\u7684\u603b\u4f53\u8868\u8fbe\u91cf\uff0c\u5e76\u8fdb\u884c\u53ef\u89c6\u5316\u3002<\/p>\n

# \u8ba1\u7b97\u6bcf\u4e2a\u6837\u672c\u7684\u603b\u4f53\u8868\u8fbe\u91cf<\/p>\n

> sample_totals <- colSums(expr_data_matrix)<\/p>\n

# \u53ef\u89c6\u5316\u6bcf\u4e2a\u6837\u672c\u7684\u603b\u4f53\u8868\u8fbe\u91cf<\/p>\n

> sample_totals_plot <- ggplot(data.frame(sample = sample_names, total_expr = sample_totals), aes(x = sample, y = total_expr)) +<\/p>\n

+ geom_bar(stat = “identity”) +<\/p>\n

+ labs(title = “Total Expression per Sample”,<\/p>\n

+ x = “Sample”,<\/p>\n

+ y = “Total Expression”)<\/p>\n

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

\"97ecee36-4c37-4a78-91bf-cafb762b8ac7\"<\/p>\n

\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528MatrixGenerics\u5305\u7684rowMeans\u548ccolSums\u51fd\u6570\u8ba1\u7b97\u4e86\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u503c\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u603b\u4f53\u8868\u8fbe\u91cf\u3002\u7136\u540e\uff0c\u6211\u4eec\u4f7f\u7528ggplot2\u5305\u8fdb\u884c\u4e86\u7b80\u5355\u7684\u53ef\u89c6\u5316\uff0c\u5206\u522b\u5c55\u793a\u4e86\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u503c\u548c\u6bcf\u4e2a\u6837\u672c\u7684\u603b\u4f53\u8868\u8fbe\u91cf\u3002<\/p>\n

\u5728\u751f\u7269\u5b66\u6570\u636e\u5206\u6790\u4e2d\uff0c\u7279\u522b\u662f\u57fa\u56e0\u7ec4\u5b66\u548c\u86cb\u767d\u8d28\u7ec4\u5b66\u7814\u7a76\u4e2d\uff0c\u6570\u636e\u96c6\u5f80\u5f80\u975e\u5e38\u5e9e\u5927\uff0c\u56e0\u6b64\u5bf9\u6027\u80fd\u7684\u8981\u6c42\u975e\u5e38\u9ad8\u3002MatrixGenerics\u901a\u8fc7\u5229\u7528\u9ad8\u6548\u7684\u5e95\u5c42\u7b97\u6cd5\u548c\u4f18\u5316\u6280\u672f\uff0c\u63d0\u4f9b\u4e86\u51fa\u8272\u7684\u6027\u80fd\u548c\u8ba1\u7b97\u6548\u7387\u3002\u8fd9\u4e3a\u751f\u7269\u5b66\u5bb6\u5904\u7406\u5927\u89c4\u6a21\u6570\u636e\u63d0\u4f9b\u4e86\u4fbf\u5229\uff0c\u4f7f\u5f97\u4ed6\u4eec\u53ef\u4ee5\u66f4\u5feb\u5730\u8fdb\u884c\u63a2\u7d22\u6027\u7814\u7a76\u3001\u6570\u636e\u53ef\u89c6\u5316\u548c\u7edf\u8ba1\u5206\u6790\u3002<\/p>\n

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305MatrixGenerics\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0c\u5b83\u7684\u901a\u7528\u6846\u67b6\u4f7f\u5f97\u5904\u7406\u4e0d\u540c\u7c7b\u578b\u7684\u77e9\u9635\u548c\u6570\u7ec4\u6570\u636e\u53d8\u5f97\u66f4\u52a0\u7b80\u5355\u548c\u9ad8\u6548\u3002\u5bf9\u4e8e\u5904\u7406\u5e9e\u5927\u7684\u751f\u7269\u5b66\u6570\u636e\u96c6\uff0c\u5b83\u7684\u4f18\u5316\u7b97\u6cd5\u548c\u9ad8\u6027\u80fd\u786e\u4fdd\u4e86\u5feb\u901f\u7684\u6570\u636e\u5904\u7406\u80fd\u529b\u3002\u5982\u679c\u4f60\u662f\u4e00\u4e2a\u751f\u7269\u5b66\u5bb6\u6216\u751f\u7269\u4fe1\u606f\u5b66\u5bb6\uff0cMatrixGenerics\u65e0\u7591\u4f1a\u662f\u4f60\u6570\u636e\u5206\u6790\u5de5\u4f5c\u4e2d\u4e0d\u53ef\u6216\u7f3a\u7684\u52a9\u624b\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:\/\/cran.r-project.org\/web\/packages\/plot.matrix\/vignettes\/plot.matrix.html<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    MatrixGenerics\u662f\u4e00\u6b3e\u5f3a\u5927\u4e14\u4e0e\u751f\u7269\u5b66\u76f8\u5173\u7684R\u8bed\u8a00\u5305\uff0c\u5b83\u662f\u7531Martin Morgan\u5728R\u8bed\u8a00\u793e\u533a\u4e2d […]<\/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\/26878"}],"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=26878"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26878\/revisions"}],"predecessor-version":[{"id":26883,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26878\/revisions\/26883"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26878"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26878"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26878"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}