More appealing plot outputs

[benc...@gmail.com]

Hello, I am trying to make more appealing figures from my results with r/qtl. I like how the plots look in qtlcharts but not sure how to export them since they are interactive plots.  Is there a way in R/qtl I can generate this kind of plot output with the threshold line or other customizations?

Also, if anyone has suggestions for how to make nicer figures from the R/qtl results please let me know!

I attached a screenshot of the output from iplotScanone

[Karl Broman]

You can use the arguments bgrect and bandcol to change the background colors, and col to change the color of the lines.

But for much further customization, you may have to edit the function. To save the function to a file use dput(qtl:::plot.scanone, "my_plot_scanone.R")

Or find it on github: https://github.com/kbroman/qtl/blob/master/R/plot.scanone.R

  data(hyper)
  hyper <- calc.genoprob(hyper, step=1)
  out <- scanone(hyper)

  plot(out, bandcol="gray80", bgrect="gray90", col="darkslateblue") 

Note also that there's a function add_threshold for adding a LOD threshold.

karl

[Ben]

I see, thanks for your fast reply!

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[Karl Broman]

Another option is to use the plotting function from R/qtl2.

  library(qtl)

  data(hyper)
  hyper <- calc.genoprob(hyper, step=1)
  out <- scanone(hyper)

  library(qtl2)

  library(qtl2convert)

  out2 <- scan_qtl_to_qtl2(out)

  plot(out2$scan1, out2$map)

karl