I often have used simple code like this to remind myself which number corresponds to which pch character:
plot(x, y, type="n", ylab="", xlab="pch", axes=FALSE)
I wondered what it would take to do the same in ggplot2. The amount of typing required to remove (most of) the y axis kinda annoys me, but otherwise, it’s quite nice:
ggplot(data.frame(x=x,y=y), aes(x=x,y=y,pch=as.factor(x))) +
xlab("pch") + ylab("") +
axis.title.y = theme_blank(),
axis.text.y = theme_blank() )
Coloc version 1.10 on CRAN. This version adds the option to calculate a credible interval for eta from its posterior distribution.
It uses a rather crude search to find the highest posterior density region, based on a numerical approximation of the posterior. The search proceeds outwards from the mode in largish steps until the desired level of the interval is exceeded, then inwards in small steps. It could certainly be optimized, but this way was quick to program and runs in a few seconds, so appeared reasonable. The calculation can be turned off by setting
bayes.ci=FALSE to speed things up when time really matters in simulations.
WGSEA version 1.07 on CRAN, small change to dependencies to require latest snpStats because of changes to the