{"id":224,"date":"2017-12-17T17:15:32","date_gmt":"2017-12-17T09:15:32","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=224"},"modified":"2017-12-17T23:18:19","modified_gmt":"2017-12-17T15:18:19","slug":"ggplot2%ef%bc%9a%e7%81%ab%e5%b1%b1%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=224","title":{"rendered":"ggplot2\uff1a\u706b\u5c71\u56fe"},"content":{"rendered":"

\u706b\u5c71\u56fe\u662f\u6563\u70b9\u56fe\u7684\u4e00\u79cd\uff0c\u4e5f\u662f\u63cf\u70b9\uff0c\u7528 geom_point()\u7ed8\u56fe<\/p>\n

1.\u52a0\u8f7d\u5305\uff0c\u8bfb\u5165\u6570\u636e\u53ca\u6570\u636e\u683c\u5f0f<\/h4>\n
library(ggplot2)\r\ndata = read.table(\"R0-vsR3.isoforms.filter.tsv\",header=T,row.names=1)<\/pre>\n
\"\"<\/p>\n
2.\u7ed8\u56fe<\/h4>\n
r03 = ggplot(data,aes(log2FC,-1*log10(FDR)))\r\nr03 + geom_point()<\/pre>\n
\"\"<\/p>\n
3.\u6539\u53d8\u70b9\u7684\u989c\u8272<\/h4>\n
r03 + geom_point(color=\"red\")\r\nr03 + geom_point(aes(color=\"red\"))\r\nr03 + geom_point(aes(color=significant)) # \u6309\u7167\u201c significant\u201d\u8fd9\u4e00\u5217\u5b9a\u4e49\u70b9\u7684\u989c\u8272\uff1b\r\n\"\"<\/pre>\n
4.\u8bbe\u7f6e\u5750\u6807\u8f74\u8303\u56f4\u548c\u6807\u9898<\/h4>\n
\u51fd\u6570xlim()\uff0cylim()\uff0c\u89c4\u5b9aX\u3001 Y\u8f74\u8303\u56f4\uff1blabs(title=\u201c..\u201d,x=\u201c..\u201d,y=\u201c..\u201d)\uff0c\u786e\u5b9a\u6807\u9898\u548c\u5750\u6807\u8f74\u6807\u7b7e\uff1bexpression\u51fd\u6570\u6539\u53d8\u6837\u5f0f\uff0c[]\u662f\u7528\u6765\u6dfb\u52a0\u4e0b\u6807\uff0c^\u662f\u7528\u6765\u6dfb\u52a0\u4e0a\u6807<\/p>\n
r03xy = r03 + geom_point(aes(color=significant)) + xlim(-4,4) + ylim(0,30)\r\nr03xy + labs(title=\"Volcano plot\",x=\"log2(FC)\")\r\nr03xy + labs(title=\"Volcano plot\",x=expression(log[2](FC)),y=expression(-log[10](FDR)))<\/pre>\n
\"\"<\/p>\n
5.\u81ea\u5b9a\u4e49\u989c\u8272<\/h4>\n
scale_color_manual(): \u81ea\u5b9a\u4e49\u989c\u8272\u914d\u8272\uff1b<\/p>\n
r03xyp = r03xy + labs(title=\"Volcano plot\",x=expression(log[2](FC)),y=expression(-log[10](FDR)))\r\nr03xyp + scale_color_manual(values = c(\"green\",\"black\", \"red\"))\r\nvolcano = r03xyp + scale_color_manual(values = c(\"#00ba38\",\"#619cff\", \"#f8766d\"))<\/pre>\n
\"\"<\/p>\n
6.\u6dfb\u52a0\u9608\u503c\u7ebf<\/h4>\n
geom_hline()\u6dfb\u52a0\u6c34\u5e73\u7ebf; geom_vline()\u6dfb\u52a0\u5782\u76f4\u7ebf<\/p>\n
volcano+geom_hline(yintercept=1.3)+geom_vline(xintercept=c(-1,1))<\/pre>\n
\"\"<\/p>\n
7.\u6539\u53d8\u7ebf\u6761\u7c7b\u578b<\/h4>\n
linetype\u53c2\u65700 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash<\/p>\n
volcano+geom_hline(yintercept=1.3,linetype=4)+geom_vline(xintercept=c(-1,1),linetype=4)<\/pre>\n
\"\"<\/p>\n
\u8be6\u7ec6\u8bb2\u89e3\u67e5\u770b\u5e2e\u52a9\u6587\u6863<\/a>\u53ca\u57fa\u8fea\u5965<\/a>\u5728\u7ebf\u89c6\u9891<\/p>\n","protected":false},"excerpt":{"rendered":"
\u706b\u5c71\u56fe\u662f\u6563\u70b9\u56fe\u7684\u4e00\u79cd\uff0c\u4e5f\u662f\u63cf\u70b9\uff0c\u7528 geom_point()\u7ed8\u56fe 1.\u52a0\u8f7d\u5305\uff0c\u8bfb\u5165\u6570\u636e\u53ca\u6570\u636e\u683c\u5f0f library(ggplot2) data = read.table(“R0-vsR3.isoforms.filter.tsv”,header=T,row.names=1) 2.\u7ed8\u56fe r03 = ggplot(data,aes(log2FC,-1*log10(FDR))) r03 + geom_point() 3.\u6539\u53d8\u70b9\u7684\u989c\u8272 r03 + geom_point(color=”red”) r03 + geom_point(aes(color=”red”)) r03 + geom_point(aes(color=significant)) # \u6309\u7167\u201c significant\u201d\u8fd9\u4e00\u5217\u5b9a\u4e49\u70b9\u7684\u989c\u8272\uff1b 4.\u8bbe\u7f6e\u5750\u6807\u8f74\u8303\u56f4\u548c\u6807\u9898 \u51fd\u6570xlim()\uff0cylim()\uff0c\u89c4\u5b9aX\u3001 Y\u8f74\u8303\u56f4\uff1blabs(title=\u201c..\u201d,x=\u201c..\u201d,y=\u201c..\u201d)\uff0c\u786e\u5b9a\u6807\u9898\u548c\u5750\u6807\u8f74\u6807\u7b7e\uff1bexpression\u51fd\u6570\u6539\u53d8\u6837\u5f0f\uff0c[]\u662f\u7528\u6765\u6dfb\u52a0\u4e0b\u6807\uff0c^\u662f\u7528\u6765\u6dfb\u52a0\u4e0a\u6807 r03xy = r03 + geom_point(aes(color=significant)) + xlim(-4,4) + ylim(0,30) r03xy + labs(title=”Volcano plot”,x=”log2(FC)”) r03xy + labs(title=”Volcano plot”,x=expression(log[2](FC)),y=expression(-log[10](FDR))) 5.\u81ea\u5b9a\u4e49\u989c\u8272 scale_color_manual(): \u81ea\u5b9a\u4e49\u989c\u8272\u914d\u8272\uff1b r03xyp = r03xy + labs(title=”Volcano […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/224"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=224"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/224\/revisions"}],"predecessor-version":[{"id":240,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/224\/revisions\/240"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=224"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=224"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=224"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}