{"id":150,"date":"2021-10-30T13:16:14","date_gmt":"2021-10-30T05:16:14","guid":{"rendered":"https:\/\/linguopeng.top\/?p=150"},"modified":"2021-10-30T13:16:15","modified_gmt":"2021-10-30T05:16:15","slug":"randombar-%e9%9a%8f%e6%9c%ba%e6%a3%ae%e6%9e%97%e4%b8%b0%e5%ba%a6-2","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=150","title":{"rendered":"random+bar-\u968f\u673a\u68ee\u6797+\u4e30\u5ea6"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>library(microeco)\r\n# use pipe operator in magrittr package\r\nlibrary(magrittr)\r\n# set.seed is used to fix the random number generation to make the results repeatable\r\nset.seed(2021)\r\n# make the plotting background same with the tutorial\r\nlibrary(ggplot2)\r\ntheme_set(theme_bw())\r\notu_table_16S_1&lt;-read.csv(\"16s.csv\",row.names = 1)\r\n#data(sample_info_16S)\r\nsample_info_16S_1&lt;-read.csv(\"SampleID.csv\",row.names = 1)\r\ntaxonomy_table_16S_1&lt;-read.csv(\"tax.csv\",row.names = 1)\r\ndataset &lt;- microtable$new(sample_table = sample_info_16S_1, \r\n                          otu_table = otu_table_16S_1,\r\n                          tax_table = taxonomy_table_16S_1)\r\n#\u7136\u540e\u4e3a\u4f7fotu_table\uff0ctax_table\u4e2d\u7684OTU\u76f8\u540c\uff0c\u4f7f\u7528tidy_dataset()\u3002\r\ndataset$tidy_dataset()\r\nprint(dataset)\r\ndataset$cal_abund()\r\nclass(dataset$taxa_abund)\r\ndir.create(\"taxa_abund\")\r\ndataset$save_abund(dirpath = \"taxa_abund\")\r\n#t1 &lt;- trans_diff$new(dataset = dataset, method = \"rf\", \r\n#                    group = \"Group\",  rf_taxa_level = \"Genus\")\r\nt1 &lt;- trans_diff$new(dataset = dataset, method = \"rf\", \r\n                     group = \"Group\",  rf_ntree = 2000,\r\n                     rf_taxa_level = \"Genus\")\r\n#t1.1&lt;-t1$res_rf\r\n#t1.1&lt;-t1$res_rf\r\n#write.csv(t1.1,\"t1.1.csv\")\r\n# t1$res_rf \u662f\u8fd9\u4e2a\u5bf9\u8c61\u7684\u5206\u7c7b\u7ed3\u679c\r\n# plot the result\r\nt2 &lt;- t1$plot_diff_abund(use_number = 1:30, \r\n                         only_abund_plot = FALSE)\r\n\r\np&lt;-gridExtra::grid.arrange(t2$p1, t2$p2, ncol=2,\r\n                           nrow = 1, widths = c(2,2))\r\np\r\n# \u4e2d\u95f4\u7684\u661f\u53f7\u4ee3\u8868\u663e\u8457\u6027\r\nggsave(\"rf.pdf\",p,width = 10,height = 8)\r\nt2.1&lt;-t2$p1$data\r\ncolnames(t2.1)&lt;-c(\"Taxa\",\"MeanDecreaseGini\",\"pvalue\")\r\nwrite.csv(t2.1,\"t2.1.csv\")\r\ndf1&lt;-read.csv(\"t2.1.csv\",row.names = 1)\r\nt2.2&lt;-t2$p2$data\r\nwrite.csv(t2.2,\"t2.2.csv\")\r\ndf2&lt;-read.csv(\"t2.2.csv\",row.names = 1)\r\n###################################################\r\ndf1&lt;-read.csv(\"t2.1.csv\",row.names = 1)\r\ndf2&lt;-read.csv(\"t2.2.csv\",row.names = 1)\r\ndf3&lt;-merge(df1,df2)\r\n#t2.1&lt;-t2$p1$data\r\n#df3$Taxa &lt;- factor(df3$Taxa, \r\n#                  levels = df3$Taxa&#91;order(df3$MeanDecreaseGini,decreasing = F)])\r\n#df3$Taxa &lt;- factor(df3$Taxa, \r\n#                   levels = df3$Taxa&#91;order(df3$MeanDecreaseGini,decreasing = F)])\r\np1 &lt;- ggplot(data = df1, mapping = aes(x=Taxa,y=MeanDecreaseGini)) +\r\n  geom_bar(stat=\"identity\",fill=\"#1E90FF\")+\r\n  coord_flip()+\r\n  theme_bw()+\r\n  theme(panel.border = element_blank(), panel.background=element_rect(fill=\"white\")) +\r\n  theme(panel.grid.minor.y = element_blank(), panel.grid.major.y = element_blank()) + #, panel.grid.minor.x = element_blank())\r\n  theme(axis.title = element_text(size = 17), axis.text.y = element_text(size = 10, color = \"black\")) +\r\n  theme(plot.margin = unit(c(.1, 0, .1, 0), \"cm\"))\r\np1\r\np2 &lt;- ggplot(df3, aes(x=Taxa, y=Mean, color = Group, fill = Group, group = Group)) +\r\n  geom_bar(stat=\"identity\", position = position_dodge(), width = .7) +\r\n  geom_errorbar(aes(ymin=Mean-SE, ymax=Mean+SE), width=.45,\r\n                position=position_dodge(.7), color = \"black\")+ \r\n  theme_bw() +\r\n  coord_flip() +\r\n  scale_color_manual(values=c(\"#80B1D3\",\"#FDB462\")) +\r\n  scale_fill_manual(values=c(\"#80B1D3\",\"#FDB462\")) +\r\n  ylab(\"Relative abundance\") +\r\n  theme(legend.position = \"right\") +\r\n  theme(panel.grid.minor.y = element_blank(), panel.grid.major.y = element_blank(), \r\n        panel.border = element_blank(), \r\n        panel.background=element_rect(fill=\"white\")) +\r\n  theme(axis.title = element_text(size = 17)) +\r\n  guides(fill=guide_legend(reverse=TRUE, ncol=1), color = FALSE) +\r\n  theme(axis.title.y=element_blank(), axis.ticks.y = element_blank(), axis.text.y = element_blank()) +\r\n  theme(plot.margin = unit(c(.1, 0, .1, 0), \"cm\"))\r\np2\r\nplot2_sig_color = \"black\"\r\nplot2_sig_size = 1.2\r\nSignificance &lt;- rev(as.character(cut(t2.1$pvalue, \r\n                                     breaks=c(-Inf, 0.001, 0.01, 0.05, Inf),\r\n                                     label=c(\"***\", \"**\", \"*\", \"\"))))\r\np2 &lt;- p2 + scale_x_discrete(labels=Significance) +\r\n  theme(axis.title.y=element_blank(), axis.ticks.y = element_blank(), \r\n        axis.text.y = element_text(color = plot2_sig_color, \r\n                                   size = rel(plot2_sig_size))) +\r\n  theme(plot.margin = unit(c(.1, 0, .1, .8), \"cm\"))\r\np3 &lt;- gridExtra::grid.arrange(p1, p2, ncol=2, nrow = 1, widths = c(2,2))\r\np3\r<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/Rplot1-1.jpeg'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"980\" height=\"455\" 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