plots: Plotting

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

Plotting

Description

Plot mapping results.

Usage

## S3 method for class 'scanOne'
plot(x,...)

plotit(lrt, cv, bychr = FALSE, chr.labels = TRUE, type = "p", lty = NULL,
   col = NULL, pch = NULL, cex = NULL, ...)

Arguments

x	Object from scanOne or scanTwo.
lrt	A data frame with (chr, dist, y,...) or (chr, dist, y, group,...), where "chr" represents chromosome, "dist" position on the chromosome, "y" the test statistic.
cv	Threshold to be drawn on the plot.
cex	See par.
bychr	A logical variable. If true, the plot will be displayed per chromosomes.
chr.labels	A logical variable. If true, the chromosome names will be drawn.
type,lty,col,pch	See plot.default.
...	Other options passed to R plot function. To call plot to plot results of scanOne, one may need to provide a genetic map gmap that should be data frame (snp, chr, dist, ...), where "snp" is the SNP (marker) name, "chr" is the chromosome where the "snp" is, and "dist" is the genetic distance in centi-Morgan (cM) from the left of the chromosome.

Note

A genetic map 'gmap' may be needed to plot an object of scanOne or scanTwo. The color option may not give what is expected.

Examples

data(miscEx)

## Not run: 
# impute missing genotypes
pheno<- pdatF8[!is.na(pdatF8$bwt) & !is.na(pdatF8$sex),]
ii<- match(rownames(pheno), rownames(gdatF8))
geno<- gdatF8[ii,]
ii<- match(rownames(pheno), rownames(gmF8$AA))
v<- list(A=gmF8$AA[ii,ii], D=gmF8$DD[ii,ii])

gdat.imp<- genoImpute(geno, gmap=gmapF8, step=Inf,
   gr=8, na.str=NA)
# estimate variance components
o<- estVC(y=pheno$bwt, x=pheno$sex, v=v)

# genome scan
llk<- scanOne(y=pheno$bwt, x=pheno$sex, vc=o, gdat=gdat.imp)

# plotting
plot(llk, gmap=gmapF8) # gmap is needed

# plotting in another way
idx<- match(colnames(gdat.imp), gmapF8$snp)
tmp<- data.frame(chr=gmapF8$chr[idx],dist=gmapF8$dist[idx],y=llk$LRT)
plotit(tmp, main="Mapping Plot", xlab="Chromosome", ylab="LRT",
   col=as.integer(tmp$ch)%%2+2,type="p")

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.