R语言处理CCK8或MTT数据，一步绘制生长曲线

Last updated on Aug 14, 2021 2 min read

CCK8数据主要是统计OD450的吸收值，一般的数据形式如下，保存为csv格式

Time	NC	NC	NC	OE	OE	OE
day1	0.549070969	0.549570976	0.547750963	0.543670962	0.536370963	0.545970956
day2	0.675742972	0.696628983	0.690574949	0.637390961	0.630422963	0.653620952
day3	0.894142977	0.884125994	0.882670941	0.82057096	0.803780962	0.819401947
day4	1.179670983	1.18457301	1.178542929	1.074040958	1.067993961	1.052209937
day5	1.505662991	1.507610027	1.500910915	1.387150955	1.32420196	1.389946927

首先我们要进行数据的预处理,把短数据转换为长数据,然后用ggpubr一步作图

cck8 <- read.csv("~/Desktop/cck8.csv") 
## 宽数据转换为长数据
library(reshape2) 
cck8_long<-melt(cck8,
                 id.vars = c('Time'),
                 variable.name='Sample',
                 value.name='OD450')
## 新增一个分组
cck8_long$Group=rep(c('control', 'treat'), each = 15)  ##分为两组，每组15个数据
### 使用ggpubr画图，可以使用prism主题
library(ggpubr)

## 载入需要的程辑包：ggplot2

library(ggprism)
ggline(cck8_long, x = "Time", y = "OD450", 
       color = "Group",shape='Group', 
       add = "mean_sd",ylab = "OD450 value",
       ggtheme = theme_prism(base_size = 12))

加个P值，调整坐标，适当美化

首先预统计看下结果,记得统计方法一定是’anova’,而不是’t.test’

compare_means(OD450~Group, data=cck8_long, group.by = "Time",method = 'anova')

## # A tibble: 5 x 7
##   Time  .y.           p   p.adj p.format p.signif method
##   <chr> <chr>     <dbl>   <dbl> <chr>    <chr>    <chr> 
## 1 day1  OD450 0.0823    0.082   0.08228  ns       Anova 
## 2 day2  OD450 0.00701   0.014   0.00701  **       Anova 
## 3 day3  OD450 0.000371  0.0015  0.00037  ***      Anova 
## 4 day4  OD450 0.0000675 0.00034 6.7e-05  ****     Anova 
## 5 day5  OD450 0.00309   0.0093  0.00309  **       Anova

结果还不错，接着添加显著标志,改色lancet配色

ggline(cck8_long, x = "Time", y = "OD450", 
       color = "Group",shape='Group', title = 'xxx cell',
       add = "mean_sd", palette = 'lancet',ylab = "OD450 value",legend = c(0.1,0.9),
       ggtheme = theme_prism(base_size = 12))+stat_compare_means(label = "p.signif",
                                                                 aes(group=Group),
                     method = "anova",  
                     hide.ns = TRUE)

- 可以调的细节还有很多,比如换个背景

ggline(cck8_long, x = "Time", y = "OD450", 
       color = "Group",shape='Group', title = 'xxx cell',
       add = "mean_sd", palette = 'lancet',ylab = "OD450 value",legend = c(0.1,0.8),
       ggtheme = theme_bw(base_size = 12))+stat_compare_means(label = "p.signif",
                                                                 aes(group=Group),
                     method = "anova",  
                     hide.ns = TRUE)

细节地方AI处理一下,当然如果你安装了esquisse，你也可以直接导出成PPT

esquisse:::ggplot_to_ppt()

## 载入需要的名字空间：rvg

## No ggplot object in environment...

R语言处理CCK8或MTT数据，一步绘制生长曲线

首先我们要进行数据的预处理,把短数据转换为长数据,然后用ggpubr一步作图

加个P值，调整坐标，适当美化

欧阳松

主治医师、讲师

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