用ggplot绘制drc

Question

我想用ggplot绘制剂量反应曲线，但当我这样做时，它看起来非常不同。是否可以用ggplot绘制曲线，因为它在使用基数R的plot函数进行轮询时看上去准确？

关于drm model摘要的第二个问题:哪个参数更能反映绑定: b、c、d或e？

library(drm)
library(ggplot2)

test_data <- data.frame(Conc = c(0.0004882812, 0.001953125 ,0.0078125, 0.03125 ,0.125 ,0.5),
                        Response = c(1.616017 ,1.165835, 0.5783709, 0.3440007, 0.2668585, 0.2336709))


## plot drm model
model_drm <- drm(Response ~ Conc, data=test_data,
                 fct=LL.4())
summary(model_drm)
plot(model_drm)


## now using ggplot

  ggplot(test_data, aes(x = Conc, y = Response )) +
  geom_point() +
  stat_smooth(method = "drm",
              method.args = list(
                fct = LL.4()),se = FALSE)

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Model fitted: Log-logistic (ED50 as parameter) (4 parms)

Parameter estimates:

                Estimate Std. Error t-value  p-value    
b:(Intercept) 1.15894518 0.08339821  13.896 0.005138 ** 
c:(Intercept) 0.24398009 0.01385086  17.615 0.003207 ** 
d:(Intercept) 1.81356338 0.05324814  34.059 0.000861 ***
e:(Intercept) 0.00261968 0.00020635  12.695 0.006148 ** 
---
Signif. codes:  
0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error:

 0.01758151 (2 degrees of freedom)

编辑：添加日志转换将导致不再绘制曲线：

ggplot(test_data, aes(x = Conc, y = Response )) +
  geom_point() +
  stat_smooth(
              method = "drm",
              method.args = list(
                fct = LL.4()
              ),
              se = FALSE
  )+
  scale_x_continuous(trans="log10")

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Answer 1

X轴需要log10缩放。此外，我们还可以重复使用已经完成的模型的计算。

ggplot(cbind(test_data, fit = fitted(model_drm)), aes(x = Conc, y = Response )) +
   geom_point() +
   geom_line(aes(y = fit)) +
   scale_x_continuous(trans = "log10")

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Answer 2

ggplot(test_data, aes(x = Conc, y = Response )) +
  geom_point() +
  geom_line(aes(y = predict(model_drm))) +
  scale_x_log10()