{"id":28227,"date":"2024-02-06T10:16:05","date_gmt":"2024-02-06T02:16:05","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28227"},"modified":"2024-02-06T10:16:06","modified_gmt":"2024-02-06T02:16:06","slug":"%e4%b8%80%e4%b8%aar%e5%8c%85%e6%90%9e%e5%ae%9a%e5%a4%9a%e7%bb%84%e5%ad%a6%e5%88%86%e6%9e%90%ef%bc%9fmixomics-%e5%a4%9a%e7%bb%84%e5%ad%a6%e6%95%b0%e6%8d%ae%e8%81%94%e5%90%88%e5%88%86%e6%9e%90-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=28227","title":{"rendered":"\u4e00\u4e2aR\u5305\u641e\u5b9a\u591a\u7ec4\u5b66\u5206\u6790\uff1fmixOmics-\u591a\u7ec4\u5b66\u6570\u636e\u8054\u5408\u5206\u6790\u4ee5\u53ca\u53ef\u89c6\u5316\u7684\u9ad8\u903c\u683c\u5de5\u5177\u5305\uff01"},"content":{"rendered":"

5\u5206\u949f\u5c31\u591f\u4e86\uff01\u5c0f\u679c\u5e26\u4f60\u7528sf\u5305\u7ed8\u5236\u53d1\u8868\u7ea7\u5730\u56fe<\/p>\n

\u5404\u4f4d\u5c0f\u4f19\u4f34\u5927\u5bb6\u597d\u554a\uff01\u5c0f\u679c\u53c8\u5e26\u7740\u597d\u4e1c\u897f\u548c\u5927\u5bb6\u89c1\u9762\u5566\uff0c\u662f\u4e0d\u662f\u5f88\u5f00\u5fc3\u5462\u3002\u51e0\u5929\u770b\u5230\u540c\u4e8b\u5229\u7528arcgis\u753b\u4e86\u4e00\u7248\u4e16\u754c\u5730\u56fe\uff0c\u68ee\u6797\u6c99\u6f20\u3001\u5c71\u5ddd\u6cb3\u6d41\u3001\u9ad8\u4f4e\u8d77\u4f0f\uff0c\u7279\u522b\u597d\u770b\uff0c\u8ba9\u5c0f\u679c\u4e5f\u662f\u5fc3\u751f\u5411\u5f80\u554a\uff01\u968f\u540e\u7acb\u523b\u8fdb\u884c\u4e86\u53cd\u601d\uff0cR\u8bed\u8a00\u80fd\u4e0d\u80fd\u8fdb\u884c\u5730\u56fe\u7684\u7ed8\u5236\u5462\uff0c\u4e0d\u5fc5\u7279\u522b\u7cbe\u7f8e\uff0c\u53ea\u9700\u8981\u5728\u8fdb\u884c\u7fa4\u4f53\u9057\u4f20\u5206\u6790\u65f6\uff0c\u5bf9\u67d0\u4e2a\u56fd\u5bb6\u3001\u67d0\u4e2a\u5730\u533a\u6216\u5168\u4e16\u754c\u7684\u533a\u57df\u8fdb\u884c\u5c55\u793a\uff0c\u968f\u540e\u4ee5\u4fbf\u5e2e\u52a9\u6211\u4eec\u8fdb\u884c\u57fa\u56e0\u6e10\u6e17\u7b49\u5206\u6790\u3002<\/p>\n

\u7687\u5929\u4e0d\u8d1f\u82e6\u5fc3\u4eba\uff0c\u5c0f\u679c\u679c\u771f\u627e\u5230\u4e86\u4e00\u6b3e\u80fd\u8fdb\u884c\u5730\u56fe\u7ed8\u5236\u7684R\u5305\u2014sf\u3002\u8fd9\u6b3eR\u5305\u7b80\u5355\u6613\u4e0a\u624b\uff0c\u5728\u4e0eggplot2\u5305\u7684\u5408\u4f5c\u4e0b\uff0c\u80fd\u6ee1\u8db3\u5bf9\u4e16\u754c\u3001\u56fd\u5bb6\u7b49\u591a\u79cd\u8303\u56f4\u7684\u7ed8\u56fe\u9700\u8981\u3002\u5728\u4f7f\u7528\u8fc7\u7a0b\u4e2d\u4ec5\u9700\u6ce8\u610f\u8981\u5c06\u8f93\u5165\u6570\u636e\u7684\u683c\u5f0f\u6539\u53d8\u6210\u2018sf\u2019\u683c\u5f0f\u5373\u53ef\u3002<\/p>\n

\u4f46\u867d\u7136\u8be5\u5305\u5728\u7a7a\u95f4\u7ed8\u56fe\u4e0a\u529f\u80fd\u5f3a\u5927\uff0c\u53ef\u662f\u5374\u4e0d\u81ea\u5e26\u753b\u4e16\u754c\u5730\u56fe\u7684\u8d44\u6599\uff0c\u56e0\u6b64\u6211\u4eec\u9700\u8981\u5bfc\u5165\u53e6\u4e00\u4e2a\u8d44\u6599\u5305\u2014rnaturalearth\uff0crnaturalearth\u63d0\u4f9b\u4e86\u7528\u4e8e\u83b7\u53d6\u548c\u64cd\u4f5c\u5168\u7403\u5730\u7406\u7a7a\u95f4\u6570\u636e\u7684\u529f\u80fd\uff0c\u4e0d\u4ec5\u514d\u8d39\uff0c\u8fd8\u5305\u542b\u5404\u4e2a\u56fd\u5bb6\u548c\u5730\u533a\u7684\u5730\u7406\u3001\u4eba\u53e3\u548c\u81ea\u7136\u73af\u5883\u7b49\u4fe1\u606f\uff0c\u80fd\u4e3a\u6211\u4eec\u5730\u56fe\u7684\u7ed8\u5236\u63d0\u4f9b\u5e2e\u52a9\u3002Rnaturalearthdata\u540c\u6837\u662f\u5e26\u6709\u4e16\u754c\u5730\u7406\u8d44\u6e90\u7684R\u5305\uff0c\u76f8\u8f83\u4e8e\u4e0a\u4e00\u4e2aR\u5305\u800c\u8a00\uff0c\u8be5\u5305\u7684\u6570\u636e\u5c06\u66f4\u4e3a\u7cbe\u7ec6\uff0c\u6240\u4ee5\u5728\u4e4b\u540e\u7ed8\u5236\u7684\u8fc7\u7a0b\u4e2d\uff0c\u5e0c\u671b\u5404\u4f4d\u5c0f\u4f19\u4f34\u6839\u636e\u81ea\u5df1\u7684\u9700\u8981\u62e9\u4f18\u800c\u9009\u54e6\u3002<\/p>\n

\u8bf4\u5b8c\u4e86\u56fe\u5f62\u7684\u7ed8\u5236\uff0c\u54b1\u4eec\u518d\u804a\u4e00\u4e0b\u5173\u4e8e\u56fe\u4f8b\u7684\u7ed8\u5236\uff0c\u4e0e\u4ee5\u5f80\u7684legend\u4e0d\u540c\uff0c\u6211\u4eec\u8fd9\u91cc\u9009\u62e9\u4f7f\u7528ggspatial\u5305\uff0c\u4ece\u540d\u5b57\u53ef\u4ee5\u770b\u51fa\uff0c\u5b83\u4e0eggplot2\u4e92\u901a\uff0c\u56e0\u6b64\u53ef\u4ee5\u5728ggplo2\u7684\u5e95\u56fe\u7684\u57fa\u7840\u4e4b\u4e0a\u589e\u52a0\u60f3\u83b7\u5f97\u7684\u6837\u5f0f\uff0c\u8ba9\u4f60\u7684\u56fe\u7247\u66f4\u4e3a\u7eda\u70c2\u591a\u5f69\u3002<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u6211\u4eec\u5e94\u7528R\u8bed\u8a00\u7ed8\u5236\u5730\u56fe\u7684\u5177\u4f53R\u5305\uff0c\u5e76\u4e14\u8fd9\u79cd\u5927\u5c3a\u5ea6\u7684\u56fe\u5f62\u4e5f\u591a\u7528\u4e8e\u7a7a\u95f4\u8f83\u5927\u7684\u6570\u636e\uff0c\u800c\u5bf9\u8fd9\u79cd\u5927\u7a7a\u95f4\u5c3a\u5ea6\u7684\u6570\u636e\uff0c\u5c0f\u679c\u66f4\u63a8\u8350\u4f7f\u7528\u670d\u52a1\u5668\u8fdb\u884c\u6570\u636e\u5904\u7406\uff0c\u5982\u679c\u5927\u5bb6\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\u7684\u8bdd\uff0c\u53ef\u4ee5\u54a8\u8be2\u5c0f\u679c\u8fdb\u884c\u670d\u52a1\u5668\u7684\u79df\u8d41\u54e6~<\/p>\n

\u597d\u5566\uff0c\u54b1\u4eec\u8bdd\u4e0d\u591a\u8bf4\uff0c\u5f00\u59cb\u4eca\u5929\u7684\u4ee3\u7801\u4ee3\u7ec3\u5427\uff01<\/p>\n

#\u8f6f\u4ef6\u5b89\u88c5\u4e0e\u8c03\u7528<\/p>\n

install.packages(c( “ggplot2”, “ggspatial”, “sf”, “rnaturalearth”, “rnaturalearthdata”))<\/p>\n

library(ggplot2)<\/p>\n

library(sf)<\/p>\n

library(rnaturalearth)<\/p>\n

library(rnaturalearthdata)<\/p>\n

library(ggspatial)<\/p>\n

#\u83b7\u5f97\u4e16\u754c\u5730\u56fe\u7684\u6570\u636e<\/p>\n

world <- ne_countries(scale = ‘medium’, #\u5730\u56fe\u8fd4\u56de\u7684\u6bd4\u4f8b\u5c3a\uff0c\u5171\u6709110, 50, 10 or ‘small’, ‘medium’, ‘large’<\/p>\n

#\u4e0a\u8ff0\u8fd4\u56de\u503c\u4e5f\u5f71\u54cd\u7740\u5730\u56fe\u6240\u83b7\u5f97\u7684\u4fe1\u606f\u7684\u591a\u4e0e\u5c11<\/p>\n

returnclass = “sf” #\u8fd4\u56de\u7ed3\u679c\u7684\u683c\u5f0f\u3002\u4e00\u822c\u9009\u62e9’sf’<\/p>\n

)<\/p>\n

<\/p>\n

\"\u56fe\u5f62\u7528\u6237\u754c\u9762\n\n\u4e2d\u5ea6\u53ef\u4fe1\u5ea6\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"<\/p>\n

\u53ef\u4ee5\u770b\u5230\uff0c\u5f53\u6211\u4eec\u9009\u62e9\u2018medium\u2019\u7c7b\u578b\u7684\u6570\u636e\u65f6\uff0c\u5171\u6709241\u521764\u884c\u7684\u6570\u636e\uff0c\u8f83\u4e4b\u2018large\u2019\u8981\u5c11\u5f88\u591a\uff0c\u8fd9\u9700\u8981\u6839\u636e\u5404\u4f4d\u5c0f\u4f19\u4f34\u7684\u753b\u56fe\u5185\u5bb9\u8fdb\u884c\u81ea\u4e3b\u9009\u62e9\u4e86\u3002<\/p>\n

class(world)<\/p>\n

<\/p>\n

\u968f\u540e\u6211\u4eec\u67e5\u770b\u4e86world\u7684\u7c7b\u578b\uff0c\u5c5e\u4e8e\u2018sf\u2019\u548c\u2018data.frame\u2019\u7c7b\u578b\uff0c\u5176\u4e2d\u7684\u2018sf\u2019\u6b63\u662f\u8be5\u5305\u753b\u56fe\u6240\u9700\u8981\u7684\u7c7b\u578b\u3002<\/p>\n

#\u7b80\u5355\u7ed8\u5236<\/p>\n

P1 <- ggplot(world) +<\/p>\n

geom_sf()<\/p>\n

P1 \"\u767d\u8272\u7684\u5730\u56fe\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"<\/p>\n

\u5982\u6b64\u5c31\u751f\u6210\u4e86\u4e00\u5f20\u4e16\u754c\u5730\u56fe\uff0c\u5982\u679c\u5404\u4f4d\u5c0f\u4f19\u4f34\u76f8\u5bf9\u5355\u4e2a\u56fd\u5bb6\u8fdb\u884c\u5730\u56fe\u7684\u7ed8\u5236\uff0c\u6211\u4eec\u53ef\u4ee5\u91c7\u7528world$name\u547d\u4ee4\u8c03\u53d6\u5404\u4e2a\u56fd\u5bb6\u7684\u540d\u79f0\u3002<\/p>\n

world$name<\/p>\n

\"\u7535\u8111\u5c4f\u5e55\u7684\u7167\u7247\u4e0a\u6709\u6587\u5b57\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"<\/p>\n

\u968f\u673a\u6311\u9009\u4e00\u4e2a\u56fd\u5bb6\uff08Thailand\uff09\u8fdb\u884c\u5730\u56fe\u7ed8\u5236<\/p>\n

Thailand <- ne_countries(scale = ‘medium’,<\/p>\n

returnclass = “sf”,<\/p>\n

country = ‘Thailand’ #\u6b64\u65f6\u5bf9\u5e94world$name\u4e2d\u7684\u8fd4\u56de\u540d<\/p>\n

)<\/p>\n

#\u521b\u5efa\u56fe\u5f62<\/p>\n

P2 <- ggplot(Thailand) +<\/p>\n

geom_sf()<\/p>\n

P2<\/p>\n

\"\u5730\u56fe\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"<\/p>\n

#\u6539\u53d8\u989c\u8272<\/p>\n

P3 <- ggplot(data = world) +<\/p>\n

geom_sf(color = “black”, fill = “darkred”)<\/p>\n

P3<\/p>\n

<\/p>\n

#\u6539\u53d8\u6e10\u53d8\u591c\u8272<\/p>\n

P4 <- ggplot(world) +<\/p>\n

geom_sf(aes(fill = pop_est)) + #pop_est\u662f\u4eba\u53e3<\/p>\n

#\u8fd9\u4e2a\u8c03\u8272\u677f\u5c5e\u4e8eviridis\u5305\u4e2d\uff0c\u8fd8\u6709magma\uff0cinferno\uff0cplasma\uff0cviridis\uff0ccividis\uff0crocket\uff0cmako<\/p>\n

scale_fill_viridis_c(option = “turbo”,<\/p>\n

#\u6839\u636e\u6570\u503c\u7684\u5e73\u65b9\u6839\u8fdb\u884c\u900f\u660e\u5ea6\u8c03\u6574\uff0c\u8fd8\u6709\u6839\u636e\u2019log\u2018\u5bf9\u6570\u8fdb\u884c\u8c03\u6574\uff0c\u6216\u8005\u9ed8\u8ba4\u4e0d\u8c03\u6574\u2018identity\u2019<\/p>\n

trans = “sqrt”)<\/p>\n

P4<\/p>\n

\"\u5730\u56fe\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"<\/p>\n

#\u5bf9\u5fc3\u4eea\u4f4d\u7f6e\u8fdb\u884c\u7ed8\u753b<\/p>\n

P5 <- ggplot(data = world) +<\/p>\n

geom_sf() +<\/p>\n

coord_sf(xlim = c(60, 140), ylim = c(0, 60), #\u7ecf\u7eac\u5ea6<\/p>\n

expand = FALSE) #\u662f\u5426\u4e0d\u7528\u7cfb\u7edf\u8fdb\u884c\u5fae\u8c03<\/p>\n

P5<\/p>\n

\"\u56fe\u793a,<\/p>\n

#\u6dfb\u52a0\u6807\u7b7e<\/p>\n

P6 <- ggplot(world) +<\/p>\n

geom_sf()+<\/p>\n

coord_sf(xlim = c(60, 140), ylim = c(0, 60),<\/p>\n

expand = FALSE) +<\/p>\n

#\u5bf9\u6807\u7b7e\u8fdb\u884c\u7ed8\u5236<\/p>\n

annotation_scale(width_hint = 0.2,location = ‘bl’) +<\/p>\n

#\u5bf9\u6307\u5411\u8fdb\u884c\u7ed8\u5236<\/p>\n

annotation_north_arrow(location = “bl”, #\u4f4d\u7f6e\uff0c\u5de6\u4e0a\u3001\u53f3\u4e0a\u3001\u53f3\u4e0b\u3001\u5de6\u4e0b<\/p>\n

which_north = “true”, #\u662f\u5426\u6307\u5411\u5317\u65b9<\/p>\n

pad_x = unit(0.25, “in”), pad_y = unit(0.5, “in”), #\u6307\u5317\u9488\u4e0e\u8fb9\u6846\u7684\u8ddd\u79bb<\/p>\n

style = north_arrow_fancy_orienteering)<\/p>\n

P6<\/p>\n

\"\u56fe\u793a,<\/p>\n

\u597d\u5566\uff0c\u4ee5\u4e0a\u5c31\u662f\u54b1\u4eec\u4eca\u5929\u7684\u5168\u90e8\u4ee3\u7ec3\u5185\u5bb9\u54e6\uff0c\u662f\u4e0d\u662f\u7279\u522b\u7b80\u5355\u5462\u3002\u5176\u5b9e\u9488\u5bf9\u8fd9\u79cd\u7b80\u5355\u7684\u3001\u6a21\u5f0f\u7684\u53ef\u89c6\u5316\u65b9\u5f0f\uff0c\u6211\u66f4\u5efa\u8bae\u5927\u5bb6\u662f\u5728\u5e94\u7528\u4e2d\u53bb\u521b\u65b0\uff0c\u5373\u591a\u5143\u5316\u5e94\u7528\u573a\u666f\u3002<\/p>\n

\u5c0f\u679c\u4e2a\u4eba\u559c\u6b22\u5728\u4e09\u4e2a\u573a\u666f\u4e2d\u4f7f\u7528\u5230\u5730\u56fe\uff0c\u4e00\u662f\u7269\u79cd\u5206\u5e03\uff0c\u5982\u5728\u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884c\u6bd4\u8f83\u65f6\uff0c\u6211\u4eec\u6240\u9009\u53d6\u7684\u7269\u79cd\u7684\u91c7\u6837\u5730\uff0c\u6216\u662f\u5728\u8d44\u6e90\u8c03\u67e5\u4e2d\u5c55\u793a\u6211\u4eec\u7684\u6837\u54c1\u6240\u5728\u5730\u3002\u53e6\u4e00\u79cd\u5c31\u662f\u5728\u7fa4\u4f53\u9057\u4f20\u5b66\u4e2d\u7684\u5e94\u7528\u4e86\uff0c\u6bd4\u5982\u5404\u4f4d\u5c0f\u4f19\u4f34\u505a\u4e86\u57fa\u56e0\u6e10\u6e17\u6216\u662f\u7fa4\u4f53\u7ed3\u6784\u5206\u6790\uff0c\u63a8\u5bfc\u51faA\u662f\u7531B\u5206\u5316\u800c\u6765\uff0c\u8fd9\u65f6\u5019\u5927\u5bb6\u53ef\u4ee5\u5728\u5730\u56fe\u4e0a\u5c55\u793a\u57fa\u56e0\u8d70\u5411\u6216\u662f\u7269\u79cd\u8fc1\u79fb\u3001\u5165\u4fb5\u65b9\u5411\u3002\u4e09\u662f\u53ef\u4ee5\u7528\u67f1\u72b6\u56fe\u6216\u997c\u56fe\u7684\u5f62\u5f0f\u5c55\u793a\u591a\u5730\u533a\u73af\u5883\u5fae\u751f\u7269\u6216\u7fa4\u843d\u7ec4\u6210\u7684\u4e0d\u540c\uff0c\u4ee5\u76f4\u89c2\u5730\u65b9\u5f0f\u5c55\u793a\u51fa\u5730\u7406\u4f4d\u7f6e\u5bf9\u7269\u79cd\u7ec4\u6210\u7684\u5f71\u54cd\u3002<\/p>\n

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