绘制大量图表

Question

我正在为我想要绘制到单个文件的许多数据集拟合剂量 - 响应曲线。

以下是一个数据集的外观：

df <- data.frame(dose=c(10,0.625,2.5,0.156,0.0391,0.00244,0.00977,0.00061,10,0.625,2.5,0.156,0.0391,0.00244,0.00977,0.00061,10,0.625,2.5,0.156,0.0391,0.00244,0.00977,0.00061),viability=c(6.12,105,57.9,81.9,86.5,98.3,96.4,81.8,27.3,85.2,80.8,92,82.5,110,90.2,76.6,11.9,89,35.4,79,95.8,117,82.1,95.1),stringsAsFactors=F)

以下是剂量反应拟合：

library(drc)
fit <- drm(viability~dose,data=df,fct=LL.4(names=c("Slope","Lower Limit","Upper Limit","ED50")))

现在我正在预测值以绘制曲线：

pred.df <- expand.grid(dose=exp(seq(log(max(df$dose)),log(min(df$dose)),length=100))) 
pred <- predict(fit,newdata=pred.df,interval="confidence") 
pred.df$viability <- pred[,1]
pred.df$viability.low <- pred[,2]
pred.df$viability.high <- pred[,3]

这就是单个情节的样子：

library(ggplot2)
p <- ggplot(df,aes(x=dose,y=viability))+geom_point()+geom_ribbon(data=pred.df,aes(x=dose,y=viability,ymin=viability.low,ymax=viability.high),alpha=0.2)+labs(y="viability")+
  geom_line(data=pred.df,aes(x=dose,y=viability))+coord_trans(x="log")+theme_bw()+scale_x_continuous(name="dose",breaks=sort(unique(df$dose)),labels=format(signif(sort(unique(df$dose)),3),scientific=T))+ggtitle(label="all doses")

在情节中添加一些参数估计值：

params <- signif(summary(fit)$coefficient[-1,1],3)
names(params) <- c("lower","upper","ed50")
p <- p + annotate("text",size=3,hjust=0,x=2.4e-3,y=5,label=paste(sapply(1:length(params),function(p) paste0(names(params)[p],"=",params[p])),collapse="\n"),colour="black")

给出了：

现在假设我有20个这样的，我想在一个图形文件中填充。

我认为合理的解决方案是使用grid.arrange：

作为一个例子，我将在这个示例数据集上循环20次：

plot.list <- vector(mode="list",20)
for(i in 1:20){
  plot.list[[i]] <- ggplot(df,aes(x=dose,y=viability))+geom_point()+geom_ribbon(data=pred.df,aes(x=dose,y=viability,ymin=viability.low,ymax=viability.high),alpha=0.2)+labs(y="viability")+
    geom_line(data=pred.df,aes(x=dose,y=viability))+coord_trans(x="log")+theme_bw()+scale_x_continuous(name="dose",breaks=sort(unique(df$dose)),labels=format(signif(sort(unique(df$dose)),3),scientific=T))+ggtitle(label="all doses")+
    annotate("text",size=3,hjust=0,x=2.4e-3,y=5,label=paste(sapply(1:length(params),function(p) paste0(names(params)[p],"=",params[p])),collapse="\n"),colour="black")
}

然后使用：

绘图

library(grid)
library(gridExtra)
grid.arrange(grobs=plot.list,ncol=3,nrow=ceiling(length(plot.list)/3)) 

这显然很难缩放。所以我的问题是如何用更好的缩放创建这个图形 - 这意味着所有对象都按比例压缩，产生一个仍然在视觉上可互换的图形。

Answer 1

您应该设置设备大小以使图表保持可读性，例如

pl = replicate(11, qplot(1,1), simplify = FALSE)
g = arrangeGrob(grobs = pl, ncol=3)
ggsave("plots.pdf", g, width=15, height=20)