Locuszoom Style Plots With User-Supplied Ld

Question

[Ryan D]

I'm a big fan of LocusZoom, but if we need to plot LD between a central SNP of interest in a population which has not been genotyped by HapMap/1kG, we are being asked to supply our own LocusZoom-style plot with LD information from our sample. For those unfamiliar with the LocusZoom plots, they are like a Manhattan of the region with recombination spots graphed, LD between an index SNP and all others shown, and genes on the bottom track. See here for an example.

Aside from downloading and installing LocusZoom on our servers, what software do you all like which can generate such a plot that gives gene-names, user-supplied LD, and shows association P-values in the manner of Locuszoom?

Thanks,

Rx

Answer 1

[Caddymob]

It's definitely not ideal, but I have done this before by plotting my own manhattan plot of SNP p-values and recombination rates from fastPHASE in R (as eps), then making the LD triangle for the region and export from Haploview (as SVG), then exporting the gene track from UCSC (as eps) and pasting it all together in illustrator. It's all vector and thus very high quality. This works fine if you just need to make a single figure, but if you have a lot to do it is really tedious - but so is the code to do this all programmatically.