用ggprism包绘制Graphpad风格的平滑曲线图

ggprism包官网给的教程中还有一个针对于GraphPad Prism示例图的绘制流程，感觉科研中还比较常用，在此记录分享一下

准备数据

# 加载R包

library(ggplot2)

library(ggprism)

library(ggnewscale)

library(dplyr)

## 准备数据

df <- data.frame(

  agonist = c(1e-10, 1e-8, 3e-8, 1e-7, 3e-7, 1e-6, 3e-6, 1e-5, 3e-5, 1e-4, 3e-4),

  ctr1 = c(0, 11, 125, 190, 258, 322, 354, 348, NA, 412, NA),

  ctr2 = c(3, 33, 141, 218, 289, 353, 359, 298, NA, 378, NA),

  ctr3 = c(2, 25, 160, 196, 345, 328, 369, 372, NA, 399, NA),

  trt1 = c(3, NA, 11, 52, 80, 171, 289, 272, 359, 352, 389),

  trt2 = c(5, NA, 25, 55, 77, 195, 230, 333, 306, 320, 338), 

  trt3 = c(4, NA, 28, 61, 44, 246, 243, 310, 297, 365, NA)

) %>% 

  mutate(log.agonist = log10(agonist)) %>% 

  pivot_longer(

    c(-agonist, -log.agonist), 

    names_pattern = "(.{3})([0-9])", 

    names_to = c("treatment", "rep"),

    values_to = "response"

  ) %>% 

  filter(!is.na(response))

## 查看数据

head(df,10)

绘制基本图形

# plot the log10(agonist concentration) vs the response

p <- ggplot(df, aes(x = log.agonist, y = response))

# define model (note x and ec50 are swapped around because ec50 is already -ve)

dose_resp <- y ~ min + ((max - min) / (1 + exp(hill_coefficient * (ec50 - x))))

# 绘制两种类型的分布曲线

p <- p + geom_smooth(

  aes(colour = treatment),

  method = "nls", formula = dose_resp, se = FALSE,

  method.args = list(start = list(min = 1.67, max = 397, ec50 = -7, hill_coefficient = 1))

)+ scale_colour_manual(

  labels = c("No inhibitor", "Inhibitor"),

  values = c("#00167B", "#9FA3FE")

)

p

## 加上散点

p <- p + ggnewscale::new_scale_colour() +

  geom_point(aes(colour = treatment, shape = treatment), size = 3) + 

  scale_colour_prism(

    palette = "winter_bright", 

    labels = c("No inhibitor",

               "Inhibitor")

  ) + 

  scale_shape_prism(

    labels = c("No inhibitor",

               "Inhibitor")

  )

p

调整主题

优化X和Y坐标轴，添加主题

## 调整Y轴坐标

p <- p + theme_prism(palette = "winter_bright", base_size = 16)+ scale_y_continuous(

  limits = c(-100, 500), 

  breaks = seq(-100, 500, 100),

  guide = "prism_offset"

)

p

## 调整X轴坐标

p <- p + scale_x_continuous(

  limits = c(-10, -3), 

  breaks = -10:-3,

  guide = "prism_offset_minor",

  minor_breaks = log10(rep(1:9, 7)*(10^rep(-10:-4, each = 9))),

  labels = function(lab) {

    do.call(

      expression,

      lapply(paste(lab), function(x) bquote(bold("10"^.(x))))

    )

  }

)

p

 ## 添加主题     

 p+ theme(

  axis.title.y = element_blank(),

  legend.title = element_blank(),

  legend.position = c(0.05, 0.95),

  legend.justification = c(0.05, 0.95)

) + 

  labs(x = "[Agonist], M")

p

     

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