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复现GMM文章的的Fig1图。 加载R包 library(tidyr)library(tidyverse)library(dplyr)library(ggsci)library(ggpubr)导入数据
所有的数据可以通过下列链接下载#xff1a;
百度网盘链接: https://pan.baidu.com/s/1isKEK1G5I6X90KYqLufmWw
提取码: t9ca
图1B
数据
…介绍
复现GMM文章的的Fig1图。 加载R包 library(tidyr)library(tidyverse)library(dplyr)library(ggsci)library(ggpubr)导入数据
所有的数据可以通过下列链接下载
百度网盘链接: https://pan.baidu.com/s/1isKEK1G5I6X90KYqLufmWw
提取码: t9ca
图1B
数据
load(01_data/plot_data/F1B.RData)head(temp)画图
temp %%mutate(typefactor(type, levelsc(Intestinal ,Metabolic , Mental , Autoimmune, Liver))) %%arrange(desc(count)) %% mutate(diseasefactor(disease, levelsunique(disease))) %%ggplot(aes(xdisease, ycount,groupdata_type)) geom_bar(statidentity,positionstack, aes(filldata_type)) geom_text(aes(labelcount),positionposition_stack(vjust 0.5),size7)facet_grid(~type, scalesfree, spacefree) theme_classic() theme(axis.text.xelement_text(angle45, hjust1,face bold,size12),axis.text.yelement_text(face bold,size12),plot.titleelement_text(hjust0.5)) ylab(No. of project) xlab(disease) coord_cartesian(ylimc(0,11),expandFALSE) scale_y_continuous(breaksseq(0, 12, 2))theme(panel.border element_blank(), axis.line element_line())scale_fill_d3(alpha 0.5)theme(text element_text(size16,face plain,family ,colour black))图1C
数据
load(01_data/plot_data/F1C.RData)head(project_stat0)project_stat0 - gather(project_stat0,phenotype,num,c(case,control))
project_stat0$phenotype - factor(project_stat0$phenotype,levels c(control,case))画图
ggdensity(project_stat0, num, colorphenotype,palette aaas,add median,alpha 0.1,size1,fill phenotype,rug TRUE)labs(x No. of samples in each cohort,yDensity)annotate(text, label paste0(Median: ,median(subset(project_stat0,phenotypecase)$num)), x 150, y 0.015, size 4, colour pal_aaas(default, alpha 0.6)(10)[2])annotate(text, label paste0(Median: ,median(subset(project_stat0,phenotypecontrol)$num)), x 150, y 0.013, size 4, colour pal_aaas(default, alpha 0.6)(10)[1])图1D
数据
load(01_data/plot_data/F1D.RData)head(auc_self)stat.test - compare_means(auc~group1,data auc_self, # group.by level,method wilcox.test) %% mutate(y.position seq(from1.05, to1.65,length.out10))
x - stat.test$p.adj
stat.test$p.adj.signif - ifelse(x0.05, ifelse(x0.01, ifelse(x0.001, ifelse(x0.0001, ****,***),**),*),ns) 画图
ggboxplot(auc_self, x group1, y auc, fill group1,palette jco,width 0.2) geom_hline(yintercept 0.5,color#dbdcdc)geom_hline(yintercept 0.6,color#ffd09a)geom_hline(yintercept 0.7,color#ffcbd8)geom_hline(yintercept 0.8,color#7b77ff)geom_hline(yintercept 0.9,color#e60020)# stat_compare_means()ylim(0.05,1.68)theme(legend.positionnone) ylab(Internal AUC)xlab()ggtitle(Disease category)theme(axis.text.xelement_text(angle20, hjust0.8,face plain,size13),text element_text(size13,face plain,family ,colour black)) stat_pvalue_manual(stat.test,label p.adj.signif)图1E
数据
load(01_data/plot_data/F1E.RData)head(self.e)stat.test - compare_means(auc~level,data self.e, # group.by level,method wilcox.test) %% mutate(y.position seq(from1.2, to1.65,length.out3))
x - stat.test$p.adj
stat.test$p.adj.signif - ifelse(x0.05, ifelse(x0.01, ifelse(x0.001, ifelse(x0.0001, ****,***),**),*),ns) 画图
ggboxplot(self.e, x level, y auc, fill level,width 0.2,palette c(#774ec7,#bd93cc,#a2c4b1))geom_hline(yintercept 0.5,color#dbdcdc)geom_hline(yintercept 0.6,color#ffd09a)geom_hline(yintercept 0.7,color#ffcbd8)geom_hline(yintercept 0.8,color#7b77ff)geom_hline(yintercept 0.9,color#e60020)ylim(0.05,1.68)# stat_compare_means()theme(legend.positionnone) ylab(Internal AUC)xlab()ggtitle(Data type)theme(axis.text.xelement_text(angle20, hjust0.8,face plain,size13),text element_text(size13,face plain,family ,colour black)) stat_pvalue_manual(stat.test,label p.adj.signif)图1F-G
数据
load(01_data/plot_data/F1FG.RData)head(a_all)画图
ggboxplot(a_all, x method, y auc, fill method,palette c(#1fb8b4,#ff7f0e),width 0.15) geom_hline(yintercept 0.5,color#dbdcdc)geom_hline(yintercept 0.6,color#ffd09a)geom_hline(yintercept 0.7,color#ffcbd8)geom_hline(yintercept 0.8,color#7b77ff)geom_hline(yintercept 0.9,color#e60020)facet_wrap(~group1,nrow 1)# annotate(text,x1:2,y0.15,labelc(0.765,0.638)) #AUCgeom_signif(comparisons list(c(internal,external)),y_position c(1.12, 1.32),test wilcox.test,map_signif_level function(x){ifelse(x0.05, ifelse(x0.01, ifelse(x0.001, ifelse(x0.0001, ****,***),**),*),ns)})ylim(0.05,1.32)theme(legend.positiontop) xlab() ylab(AUC)labs(fill AUC type)theme(text element_text(size13,face plain,family ,colour black),axis.text.x element_blank(),axis.tickselement_blank())
