How to "Create a profile LOD plot to visualize results of two-dimensional scan"?

fboehm / qtl2pleio

Testing pleiotropy vs. separate QTL in multiparental populations

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How to "Create a profile LOD plot to visualize results of two-dimensional scan"? #23

Closed HongHe0123 closed 5 years ago

HongHe0123 commented 5 years ago

The R code for "Create a profile LOD plot to visualize results of two-dimensional scan" is missing at webpage https://github.com/fboehm/qtl2pleio. Can I know how you created the figure? Thanks!

HongHe0123 commented 5 years ago

I think I figured it out :) Thanks!

temp2=tidy_scan_pvl(out, pm = DOex$pmap) temp2$marker_position=rep(DOex$pmap$3[38:(38+24)],3)

ggplot(data=temp2, aes(x = marker_position, y =lod, color = Trace, linetype=Trace) )+ geom_line() + xlab("Chromosome positon (Mb)") + ylab("LOD")

fboehm commented 5 years ago

Great! I also wrote a function plot_pvl that creates the figure. To read its help page, type ?plot_pvl at the R prompt (after loading qtl2pleio). Also, be sure to check out the vignettes to see examples of its use.