circplot

R package to facilitate making plots as circles.

Created this for the function plot_scan1_circ(), for plotting a genome scan as a circle, and for making fun of circle plots.

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Installation

Install circplot from R-universe:

install.packages("circplot", repos=c("https://kbroman.r-universe.dev",
                                     "https://cloud.r-project.org"))

Or install it from github using the remotes package:

install.packages("remotes")
library(remotes)
install_github("kbroman/circplot")

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Usage

The function xy2circ() converts (x,y) coordiates to circular coordinates. It is used internally in the function plot_scan1_circ().

library(circplot)
library(qtl)
suppressMessages(library(qtl2))
data(hyper)
hyper <- convert2cross2(hyper)

map <- insert_pseudomarkers(hyper$gmap, step=0.2)
pr <- calc_genoprob(hyper, map, err=0.01)
out <- scan1(pr, hyper$pheno)

par(mar=rep(0,4))
plot_scan1_circ(out, map, lwd=3, rlim=c(5,7))

You can also use plot_scan1_circ() to plot SNP association scans. Use altcol to have chromosomes plotted in alternating colors.

file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DO_Gatti2014/do.zip")
do <- read_cross2(file)

pr <- calc_genoprob(do, err=0.002, cores=0)
k <- calc_kinship(pr, "loco", cores=0)

variantdb <- "~/Data/CCdb/cc_variants.sqlite"
query_variants <- create_variant_query_func(variantdb)

out <- scan1spnps(pr, do$pmap, do$pheno[,1], k,
                  query_func=query_variants, cores=0,
                  Xcovar=get_x_covar(do))

lod <- out$lod
map <- qtl2:::snpinfo_to_map(out$snpinfo)

par(mar=rep(0,4))
plot_scan1_circ(lod, map, rlim=c(4,7),
                col="darkslateblue", altcol="green4",
                type="p", cex=0.4)

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License

Licensed under GPL-3.