# code chunk 0
eruptionplot = function(effectsize1,pvalue1,effectsize2,pvalue2,
	mineffect=0,minsignificance=1,...){
y1 = -log10(pvalue1); y2 = -log10(pvalue2)
plot(0,0, type = "n", ylim = c(0,max(y1,y2)),
	xlim = c(-1,1)*max(abs(range(c(effectsize1, effectsize2)))), 
	xlab = "effect size [arbitrary units]", 
	ylab = "significance [-log10 p-value]",
	lty = 0.1, lwd = 0.5, cex = 0.3)
arrows(effectsize1, y1, effectsize2, y2, length = 0.05, angle = 30, code = 2,
	col = par("fg"), lty = par("lty"), lwd = par("lwd"))
abline(v=c(0,mineffect),col="grey")
abline(h=-log10(minsignificance),col="grey")
}

# code chunk 1
library(ggplot2)
set.seed(0) # initialize random generator in order to exactly reproduce the plots here
group = as.factor(rep(c("A", "B", "C"), each = 10))
groupeffect = 5*(3-as.numeric(group))
xvar = rep(1:10,3)+groupeffect+rnorm(30,sd=1)
yvar = groupeffect+rnorm(30,sd=1)
dat = data.frame(group,xvar,yvar)

# code chunk 2
fm.1 = lm(yvar ~ xvar)
results.1 = fm.1$coefficients[2]
summary.fm.1 = summary(fm.1)
pval.1 = summary.fm.1$coefficients[2, 4]


# code chunk 3
fm.2 = lm(yvar ~ xvar + group)
results.2 = fm.2$coefficients[2]
summary.fm.2 = summary(fm.2)
pval.2 = summary.fm.2$coefficients[2, 4]

ggplot(dat, aes(x = xvar, y = yvar, color = group)) + geom_point(shape = 1) +
	scale_colour_hue(l = 50) + geom_smooth(method = lm, se = FALSE)

# code chunk 4

eruptionplot(results.1,pval.1,results.2,pval.2,minsignificance=0.05)