{"id":27510,"date":"2024-02-01T16:56:22","date_gmt":"2024-02-01T08:56:22","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27510"},"modified":"2024-02-01T16:56:24","modified_gmt":"2024-02-01T08:56:24","slug":"%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e4%b8%89%e5%88%86%e9%92%9f%e5%bf%ab%e9%80%9f%e4%bd%bf%e7%94%a8r%e8%af%ad%e8%a8%80%e5%8c%85seqlogo%e5%88%9b%e5%bb%ba%e5%a4%a7%e7%a5%9e%e7%ba%a7%e5%ba%8f%e5%88%97","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27510","title":{"rendered":"\u5c0f\u679c\u5e26\u4f60\u4e09\u5206\u949f\u5feb\u901f\u4f7f\u7528R\u8bed\u8a00\u5305seqLogo\u521b\u5efa\u5927\u795e\u7ea7\u5e8f\u5217\u6807\u8bc6\u56fe"},"content":{"rendered":"

\u5728\u751f\u7269\u5b66\u9886\u57df\uff0c\u6df1\u5165\u7814\u7a76DNA\u3001RNA\u548c\u86cb\u767d\u8d28\u5e8f\u5217\u662f\u63ed\u793a\u751f\u547d\u673a\u5236\u548c\u6f14\u5316\u8fc7\u7a0b\u7684\u5173\u952e\u4e00\u73af\u3002\u5728\u8fd9\u4e2a\u4ee4\u4eba\u7740\u8ff7\u7684\u9886\u57df\u4e2d\uff0c\u79d1\u5b66\u5bb6\u4eec\u4e0d\u65ad\u8ffd\u6c42\u66f4\u9ad8\u6548\u3001\u66f4\u51c6\u786e\u7684\u65b9\u6cd5\u6765\u89e3\u8bfb\u5e8f\u5217\u4e2d\u9690\u85cf\u7684\u4fe1\u606f\uff0c\u4ee5\u4fbf\u4e86\u89e3\u5b83\u4eec\u7684\u529f\u80fd\u3001\u7ed3\u6784\u548c\u76f8\u4e92\u4f5c\u7528\u3002\u4e3a\u4e86\u6ee1\u8db3\u8fd9\u4e00\u9700\u6c42\uff0c\u4e00\u7cfb\u5217\u5de5\u5177\u548c\u6280\u672f\u5e94\u8fd0\u800c\u751f\uff0c\u5176\u4e2d\u5728R\u8bed\u8a00\u751f\u6001\u7cfb\u7edf\u4e2d\u7684seqLogo\u5305\u5c31\u626e\u6f14\u7740\u6781\u4e3a\u91cd\u8981\u7684\u89d2\u8272\u3002seqLogo\u7684\u51fa\u73b0\uff0c\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e00\u79cd\u76f4\u89c2\u3001\u5bcc\u6709\u4fe1\u606f\u7684\u65b9\u5f0f\uff0c\u7528\u4e8e\u5c55\u793a\u5e8f\u5217\u7684\u4fdd\u5b88\u6027\u548c\u53d8\u5f02\u6027\u6a21\u5f0f\u3002<\/p>\n

seqLogo\u662f\u4e00\u6b3e\u57fa\u4e8eR\u8bed\u8a00\u7684\u5305\uff0c\u5176\u4e3b\u8981\u529f\u80fd\u5728\u4e8e\u521b\u9020\u6027\u5730\u6784\u5efa\u5e8f\u5217\u6807\u8bc6\u56fe\uff0c\u4ece\u800c\u4ee5\u89c6\u89c9\u5316\u7684\u5f62\u5f0f\u5c06\u5e8f\u5217\u5728\u4e0d\u540c\u4f4d\u7f6e\u4e0a\u7684\u7279\u5f81\u663e\u73b0\u51fa\u6765\u3002\u8fd9\u4e9b\u7279\u5f81\u4e3b\u8981\u4f53\u73b0\u5728\u5e8f\u5217\u7684\u4fdd\u5b88\u6027\u548c\u53d8\u5f02\u6027\uff0c\u5373\u5728\u4e0d\u540c\u4f4d\u7f6e\u4e0a\uff0c\u5e8f\u5217\u4e2d\u7684\u78b1\u57fa\u6216\u6c28\u57fa\u9178\u662f\u5426\u5177\u6709\u4e00\u5b9a\u7684\u4e00\u81f4\u6027\uff0c\u6216\u8005\u8868\u73b0\u51fa\u8f83\u9ad8\u7684\u591a\u6837\u6027\u3002\u8fd9\u79cd\u56fe\u5f62\u5316\u7684\u5448\u73b0\u65b9\u5f0f\u4e0d\u4ec5\u5bcc\u6709\u7f8e\u611f\uff0c\u66f4\u91cd\u8981\u7684\u662f\uff0c\u5b83\u80fd\u591f\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u8f7b\u677e\u53d1\u73b0\u4e00\u7ec4\u76f8\u5173\u5e8f\u5217\u4e2d\u7684\u91cd\u8981\u6a21\u5f0f\u548c\u8d8b\u52bf\uff0c\u8fdb\u800c\u52a0\u6df1\u5bf9DNA\u3001RNA\u548c\u86cb\u767d\u8d28\u5e8f\u5217\u751f\u7269\u5b66\u529f\u80fd\u53ca\u76f8\u4e92\u4f5c\u7528\u7684\u7406\u89e3\u3002<\/p>\n

\u5728seqLogo\u7684\u80cc\u540e\uff0c\u8574\u85cf\u7740\u4fe1\u606f\u8bba\u7684\u6838\u5fc3\u6982\u5ff5\u3002\u4fe1\u606f\u8bba\u662f\u4e00\u95e8\u7814\u7a76\u4fe1\u606f\u91cf\u548c\u4fe1\u606f\u4f20\u9012\u7684\u5b66\u79d1\uff0c\u5c06\u78b1\u57fa\u6216\u6c28\u57fa\u9178\u89c6\u4e3a\u4fe1\u606f\u7684\u57fa\u672c\u5355\u5143\uff0c\u8003\u5bdf\u5b83\u4eec\u5728\u7279\u5b9a\u4f4d\u7f6e\u4e0a\u51fa\u73b0\u7684\u6982\u7387\u5206\u5e03\u3002seqLogo\u5de7\u5999\u5730\u5c06\u4fe1\u606f\u8bba\u5f15\u5165\u5e8f\u5217\u5206\u6790\u4e2d\uff0c\u901a\u8fc7\u8ba1\u7b97\u6bcf\u4e2a\u4f4d\u7f6e\u4e0a\u7b26\u53f7\u7684\u9891\u7387\u548c\u76f8\u5bf9\u9891\u7387\uff0c\u63ed\u793a\u5e8f\u5217\u4e2d\u7684\u6a21\u5f0f\u3002\u8fd9\u4e00\u8fc7\u7a0b\u4e2d\uff0c\u6bcf\u4e2a\u4f4d\u7f6e\u4e0a\u7684\u7b26\u53f7\u9891\u7387\u88ab\u8f6c\u6362\u6210\u4fe1\u606f\u71b5\uff0c\u5373\u4fe1\u606f\u7684\u4e0d\u786e\u5b9a\u7a0b\u5ea6\u3002\u4fe1\u606f\u71b5\u4f4e\u7684\u4f4d\u7f6e\u8868\u660e\u5e8f\u5217\u5728\u6b64\u5904\u76f8\u5bf9\u4fdd\u5b88\uff0c\u800c\u9ad8\u7684\u4fe1\u606f\u71b5\u5219\u610f\u5473\u7740\u591a\u6837\u6027\u8f83\u5927\uff0c\u53d8\u5f02\u6027\u8f83\u9ad8\u3002<\/p>\n

seqLogo\u7684\u5de5\u4f5c\u6d41\u7a0b\u4fa7\u91cd\u4e8e\u5206\u6790\u5e8f\u5217\u4e2d\u6bcf\u4e2a\u4f4d\u7f6e\u7684\u7b26\u53f7\u9891\u7387\u548c\u4fe1\u606f\u71b5\u3002\u5bf9\u4e8e\u4e00\u7ec4\u76f8\u5173\u5e8f\u5217\uff0cseqLogo\u5c06\u5b83\u4eec\u7edf\u4e00\u8f6c\u6362\u6210\u4e00\u4e2a\u5e8f\u5217\u96c6\u5408\uff0c\u5e76\u8fd0\u7528\u4fe1\u606f\u71b5\u7684\u6982\u5ff5\u5448\u73b0\u4e0d\u540c\u4f4d\u7f6e\u4e0a\u7684\u5e8f\u5217\u6a21\u5f0f\u3002\u5728\u751f\u6210\u7684\u56fe\u8868\u4e2d\uff0c\u6bcf\u4e2a\u4f4d\u7f6e\u4e0a\u7684\u7b26\u53f7\u5c06\u88ab\u5206\u914d\u4e00\u4e2a\u9ad8\u5ea6\uff0c\u8be5\u9ad8\u5ea6\u53d6\u51b3\u4e8e\u4f4d\u7f6e\u4e0a\u7684\u4fe1\u606f\u71b5\u548c\u76f8\u5bf9\u9891\u7387\u3002\u8fd9\u79cd\u8bbe\u8ba1\u4f7f\u5f97\u56fe\u8868\u80fd\u591f\u5c06\u4fdd\u5b88\u6027\u9ad8\u7684\u4f4d\u7f6e\u5c55\u793a\u4e3a\u8f83\u9ad8\u7684\u7b26\u53f7\uff0c\u800c\u8f83\u4e0d\u4fdd\u5b88\u7684\u4f4d\u7f6e\u5219\u8868\u73b0\u4e3a\u8f83\u77ed\u7684\u7b26\u53f7\u3002<\/p>\n

\u4f7f\u7528seqLogo\u5305\u7684\u6b65\u9aa4\u76f8\u5bf9\u7b80\u5355\u3002\u9996\u5148\uff0c\u4f60\u9700\u8981\u5728R\u4e2d\u5b89\u88c5\u5e76\u52a0\u8f7d\u8be5\u5305\uff0c\u7136\u540e\u51c6\u5907\u76f8\u5173\u5e8f\u5217\u6570\u636e\u3002seqLogo\u652f\u6301DNA\u3001RNA\u548c\u86cb\u767d\u8d28\u5e8f\u5217\uff0c\u4f60\u53ef\u4ee5\u6839\u636e\u9700\u8981\u9009\u53d6\u76f8\u5e94\u7684\u6570\u636e\u96c6\u3002\u63a5\u7740\uff0c\u5c06\u8fd9\u4e9b\u5e8f\u5217\u8f6c\u6362\u6210\u9002\u7528\u4e8eseqLogo\u7684\u683c\u5f0f\uff0c\u4f8b\u5982DNAStringSet\u5bf9\u8c61\uff0c\u4e4b\u540e\u901a\u8fc7\u7ed8\u56fe\u51fd\u6570\u5373\u53ef\u5f97\u5230\u5e8f\u5217\u6807\u8bc6\u56fe\u3002\u6807\u8bc6\u56fe\u4e2d\u7684\u6bcf\u4e2a\u4f4d\u7f6e\u90fd\u5c06\u4ee5\u5176\u4fe1\u606f\u71b5\u548c\u76f8\u5bf9\u9891\u7387\u4e3a\u57fa\u7840\u5206\u914d\u76f8\u5e94\u7684\u7b26\u53f7\uff0c\u4ece\u800c\u5f62\u6210\u56fe\u5f62\u5316\u5c55\u793a\u3002<\/p>\n

\u8981\u4f7f\u7528seqLogo\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“seqLogo”) #\u5b89\u88c5seqLogo\u8bed\u8a00\u5305<\/p>\n

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

\u901a\u8fc7\u5c06\u4fe1\u606f\u71b5\u8f6c\u5316\u4e3a\u53ef\u89c6\u5316\u56fe\u5f62\uff0cseqLogo\u4ee5\u5176\u72ec\u7279\u800c\u751f\u52a8\u7684\u65b9\u5f0f\u5448\u73b0\u4e86\u5e8f\u5217\u5728\u4e0d\u540c\u4f4d\u7f6e\u4e0a\u7684\u6a21\u5f0f\uff0c\u4ece\u800c\u4e3a\u751f\u7269\u5b66\u7814\u7a76\u63d0\u4f9b\u4e86\u6781\u5927\u7684\u6d1e\u5bdf\u529b\u3002\u5728\u8fd9\u4e2a\u5f15\u4eba\u5165\u80dc\u7684\u56fe\u5f62\u4e2d\uff0c\u6bcf\u4e2a\u5e8f\u5217\u4f4d\u7f6e\u90fd\u88ab\u8d4b\u4e88\u4e86\u4e00\u4e2a\u89c6\u89c9\u9ad8\u5ea6\uff0c\u8fd9\u4e2a\u9ad8\u5ea6\u662f\u6839\u636e\u5176\u4fe1\u606f\u71b5\u548c\u76f8\u5bf9\u9891\u7387\u8ba1\u7b97\u5f97\u51fa\u7684\u3002\u8fd9\u79cd\u7cbe\u5de7\u7684\u8bbe\u8ba1\u4f7f\u5f97\u56fe\u5f62\u6210\u4e3a\u4e00\u4e2a\u89c6\u89c9\u56fe\u666f\uff0c\u51c6\u786e\u5730\u4f20\u8fbe\u4e86\u5e8f\u5217\u4e2d\u7684\u6a21\u5f0f\u4fe1\u606f\uff0c\u4f7f\u4eba\u4eec\u80fd\u591f\u4e00\u76ee\u4e86\u7136\u5730\u8bc6\u522b\u51fa\u4fdd\u5b88\u6a21\u5f0f\u548c\u53d8\u5f02\u6a21\u5f0f\uff0c\u4e3a\u8fdb\u4e00\u6b65\u7684\u751f\u7269\u5b66\u89e3\u91ca\u548c\u7814\u7a76\u63d0\u4f9b\u4e86\u6709\u529b\u7684\u5de5\u5177\u3002<\/p>\n

\u5728\u751f\u6210\u7684\u56fe\u8868\u4e2d\uff0c\u8f83\u4e3a\u4fdd\u5b88\u7684\u4f4d\u7f6e\u5c06\u5448\u73b0\u51fa\u66f4\u9ad8\u7684\u7b26\u53f7\uff0c\u8fd9\u662f\u56e0\u4e3a\u8fd9\u4e9b\u4f4d\u7f6e\u4e0a\u7684\u7b26\u53f7\u5177\u6709\u8f83\u4f4e\u7684\u4fe1\u606f\u71b5\u3002\u4fdd\u5b88\u6027\u9ad8\u7684\u4f4d\u7f6e\u610f\u5473\u7740\u5728\u8fd9\u4e9b\u4f4d\u7f6e\u4e0a\uff0c\u5e8f\u5217\u4e2d\u7684\u7b26\u53f7\u503e\u5411\u4e8e\u76f8\u5bf9\u4e00\u81f4\u5730\u51fa\u73b0\uff0c\u5f62\u6210\u4e86\u7a33\u5b9a\u7684\u5e8f\u5217\u6a21\u5f0f\u3002\u8fd9\u79cd\u6a21\u5f0f\u5f80\u5f80\u4e0e\u751f\u7269\u5b66\u529f\u80fd\u5bc6\u5207\u76f8\u5173\uff0c\u4f8b\u5982\u5728\u86cb\u767d\u8d28\u7ed3\u6784\u4e2d\u7684\u4fdd\u5b88\u4f4d\u70b9\uff0c\u6216\u8005\u5728\u57fa\u56e0\u7684\u542f\u52a8\u5b50\u533a\u57df\u4e2d\u7684\u4fdd\u5b88DNA\u5e8f\u5217\u3002\u56fe\u8868\u4e2d\u9ad8\u5ea6\u7684\u589e\u52a0\u4f7f\u5f97\u8fd9\u4e9b\u4fdd\u5b88\u6a21\u5f0f\u80fd\u591f\u5f15\u4eba\u6ce8\u76ee\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u51c6\u786e\u5730\u8bc6\u522b\u51fa\u5177\u6709\u91cd\u8981\u751f\u7269\u5b66\u529f\u80fd\u7684\u5e8f\u5217\u7247\u6bb5\u3002<\/p>\n

\u4e0e\u6b64\u76f8\u53cd\uff0c\u5728\u56fe\u8868\u4e2d\uff0c\u8f83\u4e0d\u4fdd\u5b88\u7684\u4f4d\u7f6e\u5c06\u8868\u73b0\u4e3a\u66f4\u77ed\u7684\u7b26\u53f7\uff0c\u56e0\u4e3a\u8fd9\u4e9b\u4f4d\u7f6e\u4e0a\u7684\u7b26\u53f7\u5177\u6709\u8f83\u9ad8\u7684\u4fe1\u606f\u71b5\u3002\u8fd9\u8868\u793a\u5728\u8fd9\u4e9b\u4f4d\u7f6e\u4e0a\uff0c\u5e8f\u5217\u7684\u53d8\u5f02\u6027\u8f83\u5927\uff0c\u7b26\u53f7\u7684\u51fa\u73b0\u76f8\u5bf9\u4e0d\u7a33\u5b9a\u3002\u8fd9\u4e9b\u53d8\u5f02\u6a21\u5f0f\u53ef\u80fd\u4e0e\u4e0d\u540c\u7269\u79cd\u3001\u4e9a\u578b\u6216\u53d8\u5f02\u6709\u5173\uff0c\u4e5f\u53ef\u80fd\u4ee3\u8868\u4e86\u5e8f\u5217\u4e2d\u7684\u65e0\u5e8f\u533a\u57df\u3002\u56fe\u8868\u4e2d\u7684\u8fd9\u79cd\u77ed\u7b26\u53f7\u53ef\u4ee5\u5feb\u901f\u5438\u5f15\u6ce8\u610f\u529b\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u786e\u5b9a\u5e8f\u5217\u4e2d\u7684\u8fd9\u4e9b\u53d8\u5f02\u6a21\u5f0f\uff0c\u8fdb\u800c\u63a2\u7d22\u5176\u5728\u751f\u7269\u5b66\u4e0a\u7684\u6f5c\u5728\u610f\u4e49\u3002<\/p>\n

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

#\u9996\u5148\uff0c\u786e\u4fdd\u4f60\u5df2\u7ecf\u5b89\u88c5\u4e86seqLogo\u5305<\/p>\n

> install.packages(“seqLogo”)<\/p>\n

#\u4e24\u4e2aDNA\u5e8f\u5217\u4f5c\u4e3a\u793a\u4f8b\u6570\u636e<\/p>\n

> sequence1 <- “ATGCTAAGCGTA”<\/p>\n

> sequence2 <- “ATGCAAAGCGTA”<\/p>\n

# \u5bfc\u5165seqLogo\u5305<\/p>\n

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

# \u521b\u5efa\u5e8f\u5217\u96c6\u5408<\/p>\n

> sequences <- c(sequence1, sequence2)<\/p>\n

# \u5c06\u5e8f\u5217\u96c6\u5408\u8f6c\u5316\u4e3aDNAStringSet\u5bf9\u8c61<\/p>\n

> seq_set <- DNAStringSet(sequences)<\/p>\n

# \u521b\u5efa\u5e8f\u5217\u6807\u8bc6\u56fe<\/p>\n

> logo <- seqLogo(seq_set)<\/p>\n

# \u663e\u793a\u5e8f\u5217\u6807\u8bc6\u56fe<\/p>\n

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

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

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References:<\/p>\n

    \n
  1. https:\/\/bioconductor.org\/packages\/devel\/bioc\/vignettes\/seqLogo\/inst\/doc\/seqLogo.html<\/a><\/li>\n
  2. https:\/\/davetang.org\/muse\/2013\/01\/30\/sequence-logos-with-r\/<\/a><\/li>\n
  3. https:\/\/stackoverflow.com\/questions\/5438474\/plotting-a-sequence-logo-using-ggplot2<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

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