R: Graphical linkage group identity and alignment.
alignCross
R Documentation
Graphical linkage group identity and alignment.
Description
A graphical tool for identity and alignment of linkage groups in qtl
cross objects using reference maps.
Usage
alignCross(object, chr, maps, ...)
Arguments
object
A qtl cross object with any class structure.
chr
A character string of linkage group names or a logical vector equal to
the length of the number of linkage groups (see subset.cross).
maps
A named list of qtl cross objects or data.frame objects
containing markers that are present in object. The matching
markers are used to identify and orient the object linkage groups (see Details).
...
Other arguments to be passed to the high level lattice plot.
Details
If any list elements of map are qtl"cross" objects
then marker names, linkage group identity and genetic distance
information are extracted. List elements of map that are data.frame
objects must explicitly contain named columns
"marker","ref.chr","ref.dist" otherwise an error will be produced.
For each linkage group determined by chr, the contents of the
listed maps are checked for matching markers in
object. For each chr and reference map combination, a
scatter plot of the object genetic distances against the
reference distances is displayed with reference
linkage group names as the plotting character. If a linkage group is in
correct orientation the overall slope of the scatter plot should be
positive. If a linkage group requires inverting then the overall slope
should be negative.
Value
A lattice panel plot is displayed with panels labelled by a combination
of chr and the maps used as a reference. A data frame of
these results is also invisibly returned.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ASMap)
Loading required package: qtl
Loading required package: gtools
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
# maps v3.1: updated 'world': all lakes moved to separate new #
# 'lakes' database. Type '?world' or 'news(package="maps")'. #
Loading required package: RColorBrewer
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ASMap/alignCross.Rd_%03d_medium.png", width=480, height=480)
> ### Name: alignCross
> ### Title: Graphical linkage group identity and alignment.
> ### Aliases: alignCross
> ### Keywords: misc
>
> ### ** Examples
>
>
> data(mapDH, package = "ASMap")
>
> chrl <- sample(c(TRUE,FALSE), 23, replace = TRUE)
> mapDH1 <- subset(mapDH, chr = chrl)
> alignCross(mapDH, maps = list(DH = mapDH1), layout = c(3,5), col = 1:7)
>
>
>
>
>
>
> dev.off()
null device
1
>