cad metabolites

cad_metab_forestplot.R

library(ggplot2)
library(ggthemes)
library(readxl)

b <- read_excel("~/Downloads/CAD-metabolites-3-way-comparison.xlsx", skip=1)
b <- b[!is.na(b$exposure), ]
names(b) <- gsub("-", "\\.", names(b))
b$obs.logOR <- log(b$obs.OR)
b$obs.SE <- NA

b1 <- subset(b, select=c(exposure, catalog, LDSC.rg, LDSC.se))
b2 <- subset(b, select=c(exposure, catalog, MR.beta, MR.SE))
b3 <- subset(b, select=c(exposure, catalog, obs.logOR, obs.SE))

names(b1) <- names(b2) <- names(b3) <- c("exposure", "catalog", "eff", "se")
b1$test <- "LDSC"
b2$test <- "MR"
b3$test <- "Obs"

b <- rbind(b1, b2, b3)


ggplot(b, aes(y=eff, x=test)) +
geom_hline(yintercept=0) +
geom_point(aes(colour=test), position=position_dodge(width=2), size=3) +
geom_errorbar(aes(colour=test, ymin=eff-1.96*se, ymax=eff+1.96*se), width=0, position=position_dodge(width=2), size=2) +
scale_colour_brewer(type="qual") +
facet_grid(exposure ~ .) +
coord_flip() +
theme(strip.text.y = element_text(hjust=0, angle = 0), axis.text.y=element_blank(), axis.ticks.y=element_blank())