R: Plotting

plotit {QTLRel} | R Documentation

## 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$dist[idx],y=llk$p)
    plotit(tmp, main="Mapping Plot", xlab="Chromosome", ylab="LRT",
       col=as.integer(tmp$ch)%%2+2,type="p")

    ## End(Not run)

[Package QTLRel version 1.0 Index]