Can I calculate p-value with mean and se values in facet_wrap?

Question

How can I calculate p-value from sample mean and se? Thanks for your help.

Below is the code that I am using.

ggplot(combine_mean_se2, aes(x=Treatment, y=mean, colour=Treatment)) +
  geom_point(size=6)+
  geom_linerange(aes(ymin= mean-se, ymax=mean+se), colour="grey10", linewidth=1) +
  #scale_color_manual(values=c("firebrick4", "dodgerblue4")) +
  ylab("Feature Mean and SE") + 
  xlab("") +
  facet_wrap(~traits, scales = "free") + 
  elitetheme2 + 
  theme(legend.position = "top",
        strip.text.x = element_text(size = 21, face = "bold")) 

here is my data

https://docs.google.com/spreadsheets/d/1q1guxAKosKztNXWO3ey1ZKZm4VU49ub58_C_bZ8TO1k/edit#gid=0

Answer 1

You already calculated the mean and se. It would be best if you had each sample value for statistical testing. The ggpubr package has excellent functions to add p-value and SE in your graphs.

http://www.sthda.com/english/wiki/one-way-anova-test-in-r

Answer 2

I may not be correct on this p value, but please let me know if it isn't and let me know any formula to derive the p value

I used the below formula

z = Est/SE P = exp(−0.717×z − 0.416×z^2)

code

library(rvest)
library(tidyverse)

df <- rvest::read_html('https://docs.google.com/spreadsheets/d/1q1guxAKosKztNXWO3ey1ZKZm4VU49ub58_C_bZ8TO1k/edit#gid=0') %>% html_table()
df2 <- df[[1]][2:17,2:6]
nam <- df[[1]][1,2:6]
nam2 <- (nam %>% pivot_longer(c('A','B','C','D','E')))$value

names(df2) <- nam2
df3 <- df2 %>% mutate(mean=as.numeric(mean), se=as.numeric(se), z=mean/se, 
p=exp(-0.717*z-0.416*z^2)) 

output

# A tibble: 16 × 7
   Treatment Si    traits   mean    se     z         p
   <chr>     <chr> <chr>   <dbl> <dbl> <dbl>     <dbl>
 1 K-C       0mM   TRL    12246.  861. 14.2  1.08e- 41
 2 K-CSi     4mM   TRL    16164.  979. 16.5  4.38e- 55
 3 K-DS      0mM   TRL     7852.  525. 14.9  9.67e- 46
 4 K-DSSi    4mM   TRL    12417. 1039. 12.0  2.94e- 30
 5 R-C       0mM   TRL    15893.  638. 24.9  1.59e-120
 6 R-CSi     4mM   TRL    23529. 1001. 23.5  6.29e-108
 7 R-DS      0mM   TRL    10988.  312. 35.2  5.44e-236
 8 R-DSSi    4mM   TRL    14063.  818. 17.2  1.70e- 59
 9 K-C       0mM   PRL     6620.  903.  7.33 9.91e- 13
10 K-CSi     4mM   PRL     9237.  662. 14.0  2.96e- 40
11 K-DS      0mM   PRL     3779.  408.  9.26 4.16e- 19
12 K-DSSi    4mM   PRL     6752.  657. 10.3  5.32e- 23
13 R-C       0mM   PRL     9882.  366. 27.0  3.64e-141
14 R-CSi     4mM   PRL    13409. 1138. 11.8  1.87e- 29
15 R-DS      0mM   PRL     5605.  275. 20.4  2.72e- 82
16 R-DSSi    4mM   PRL     8652.  618. 14.0  1.58e- 40