P-value function via Fisher's exact test

pfun_fisher.R

library(MCMCpack)
library(exact2x2)
library(ggplot2)
library(patchwork)

X <-matrix(c(12,5,6,12), nrow=2)
fpfun <- function(phi){exact2x2::exact2x2(x=X, or=exp(phi))$p.value}
rs <- rowSums(X)
cs <- colSums(X)
flfun <- function(phi){MCMCpack::dnoncenhypergeom(x = X[1,1], cs[1],cs[2],rs[1], exp(phi))}

phi <- seq(-10,10,by=0.1)
pv <-sapply(phi, fpfun)
lv <-sapply(phi, flfun)

df <- data.frame(logOR =phi, pvalue=pv, likelihood=lv)

p1 <- ggplot(df,aes(x=logOR))+
  geom_line(aes(y=pvalue))+
  theme_bw()

p2 <- ggplot(df,aes(x=logOR))+
  geom_line(aes(y=likelihood))+
  theme_bw()

p1/p2
#ggsave("pfun_fisher.png")