overlay QTL plots

[Mingzi Xu]

Dear all,

I would like to show both interval mapping and multiple QTL mapping figures in a paper. With many families, if I show each in separate figures, that would result in many figures. I'm wondering if there is a way to overlay multiple QTL mapping LOD profile on top of certain chromosomes in interval mapping in R/qtl or other softwares, given that not all chromosomes have a significant peak in the multiple QTL model. I tried simply cut and paste and visually align the markers. The result isn't very visually appealing because one figure has to be stretched or squeezed. 

Many thanks!

Mingzi

[Karl Broman]

You should be able to overlay the single-QTL scan by using plot() with add=TRUE.
Here's an example.

data(hyper)
hyper <- calc.genoprob(hyper, step=1)
out <- scanone(hyper)
qtl <- makeqtl(hyper, chr=c(1,4), pos=c(48.3, 29.5), what="prob")
qtl <- refineqtl(hyper, qtl=qtl, method="hk")

# just show chr 1 and 4
plotLodProfile(qtl)
plot(out, chr=c(1,4), add=TRUE, col="gray")

# show all chromosomes
plotLodProfile(qtl, showallchr=TRUE)
plot(out, add=TRUE, col="gray")

karl

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[Mingzi Xu]

Thank you so much! This is exactly what I'm looking for!

[bmu...@ncsu.edu]

Hi,

I have a similar question. but with the function plot(qtl). I have 2 set of qtl derived from different models and I would like to show both with different colors on the same map. I tried the add fuction but did not worked, 

> plot(qtl.122, col="blue")

> plot(qtl.121, add=TRUE, col="red")

How can I overlay both sets?

Thank you,

[Karl Broman]

There's not a simple way to do this at present, unfortunately.

But you could combine the two QTL into one object and then use a vector of colors.

qtl_combined <- qtl.122
for(i in 1:nqtl(qtl.121)) {
qtl_combined <- addtoqtl( mycross, qtl_combined, qtl.121$chr[i], qtl.121$pos[i], qtl.121$name[i] )
qtl_combined$altname[nqtl(qtl_combined)] <- qtl.121$altname[i]
}

plot(qtl_combined, col=rep(c("blue", "red"), c(nqtl(qtl.122), nqtl(qtl.121)))

karl

[bmu...@ncsu.edu]

thank you very much

Bryan

[John Lovell]

You can check out qtlTools::segmentsOnMap

https://lovelleeb.weebly.com/qtltools/plot-qtl-confidence-intervals-on-a-genetic-map-with-qtltools