RgeneticMap

A R function to draw genetic maps (linkage map), and can be used with R/qtl directly.
You can export the maps as svg format and edit them with any svg editor (Inkscape is a good FREE svg editor).

Example

library(qtl)
data("hyper")
summary(hyper)

source("linkmap.R")
linkmap(hyper,chr=c(1,2,3))

pdf(file="geneticMap.pdf",paper="USr")
linkmap(hyper,chr=c(1,2))
linkmap(hyper,chr=c(1,2,3))
linkmap(hyper,chr=c(1,2,3,4))
dev.off()

# Absolute positions
svg(file="GeneticMap.svg", width=7, height=7, bg=NA)
linkmap(hyper,chr=c(1,2,3), ruler = T, m.cex = 0.8)
dev.off()

# Relative positions
svg(file="GeneticMap-interval.svg", width=7, height=7, bg=NA)
linkmap(hyper,chr=c(1,2,3), ruler = T, m.cex = 0.8, interval=T)
dev.off()

SVG format output example

Absolute positions

Relative positions

Parameters

linkmap <- function(object, chr, chr.space = 2, m.cex = 0.6, interval = FALSE, ruler = FALSE, ...){...}

Input of this function:

• object:
  • a "cross" object from R/qtl
  • a "map" class from the output of "pull.map" in R/qtl
  • a data frame with marker column, chromosme column and position column named as "mar", "chr" and "pos", respectively
• chr: a vector of chromosome names that need to be drawn.
• chr.space: space between each chromosomes
• m.cex: font size
• interval: NULL/TRUE/FALSE: plot no distance/marker interval/absolute distance. Default is absolute distance.
• ruler: whether to draw ruler on the left
• ...: other plot parameters

Credits

This script is a modification of function "link.map.cross" in R package "wgaim" (https://cran.r-project.org/web/packages/wgaim/index.html). I added marker positions on the left side of the chromosomes and make it look better.

Other genetic map packages in R

• LinkageMapView: Plot Linkage Group Maps with Quantitative Trait Loci (https://cran.r-project.org/web/packages/LinkageMapView/index.html) [Right now it can only export pdf format]