Comparing Genetic Maps

[Joshua Havill]

Hi Karl,

I am comparing parental maps, by visualizing anchor marker order between each parental group using the plotMap() function.

The graphics device appears to plot the same map comparison twice as opposed to a larger single image. I have refreshed my R session, used dev.off(), etc. But it's still plotting the same map comparison twice as if par(mfrow=c(2,1)) was being enforced.

Thoughts of getting it to plot just one map?

[Karl Broman]

Can you show the code you’re using?

karl

On Jan 4, 2022, at 3:38 PM, 'Joshua Havill' via R/qtl discussion <rqtl...@googlegroups.com> wrote:



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[Joshua Havill]

Hi Karl,

plotMap(four_way, four_way_p2)

four_way is a cross object with 10 LGs for one parent.

four_way_p2 is a cross object with 10 LGs for the second.

A number of markers are specific to each parent but common between both parents.

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Joshua Havill, M. Sc.
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Graduate Research Assistant, Ph. D. Candidate

Plant and Microbial Biology Graduate Program

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[Joshua Havill]

plotMap() or plot.map() both produce a single large image of the genetic map when either cross is specified but when both crosses are included, two smaller versions of the same map comparison are produced, one on top of the other.

[Karl Broman]

With a 4-way cross, there are sex-specific maps. And so the comparison of two maps will be in two panels. The top panel compares the two female maps and the bottom panel compares the two male maps.

Here's an example:

library(qtl)

data(fake.4way)

newmap <- est.map(fake.4way)

plotMap(fake.4way, newmap)

Compare that result to the individual maps:

plotMap(fake.4way)

plotMap(newmap)

karl

[Joshua Havill]

Hi Karl,

I separated each parental map into a separate cross. What is the appropriate way to import or specify that one set of groups is specific to one sex versus the other?

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[Karl Broman]

I'm not sure. I don't really understand what that means.

In a 4-way cross, the genetic map is a list of matrices each with two rows.

You can pull them apart with lapply().

library(qtl)

data(fake.4way)

map <- pull.map(fake.4way)

female_map <- lapply(map, "[", 1, )

male_map <- lapply(map, "[", 2, )

karl

[havi...@umn.edu]

Hi Karl,

I built each parental map with lm x ll (maternally segregating) or nn x np (paternally segregating markers. Included in each group were sets of common “intercross” markers, hk x hk.

So one parent has lm x ll and hk x hk markers. The other parent has nn x np and hk x hk markers. The hk x hk are common between both parents/maps, thus allowing one to compare the relative order between the two maps.

These were imported as separate cross objects, because of issues with visualizing RF matrices between parental meioses.

The 4WC was still used because it considered marker phase as estimated originally by JoinMap.

-------

Joshua Havill

612-836-7834

On Jan 4, 2022, at 5:03 PM, Karl Broman <kbr...@gmail.com> wrote:



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