plotprofile: Plot profile LOD matrix.

In ikwak2/funqtl: QTL Mapping for Function-Valued Traits

Plot profile LOD matrix.

Description

Plot profile LOD matrix of given multiple QTL model.

Usage

plotprofile(
  lodmatlist,
  times,
  ylab = "QTL position",
  xlab = "Time",
  mval = 0,
  ...
)

Arguments

lodmatlist	An "lodprofileM" object as produced by getprofile
times	A vector of times at which the phenotypes were measured.
ylab	A label of y. Default is "QTL position".
xlab	A label of x. Default is "Time".
mval	The maximum LOD value of legend. The color of legend goes 0 to mval. If this value is less than the maximum LOD score, it is automatically changed to that maximum.
...	Additional graphical components, passed to image.plot.

Value

None.

Author(s)

Il-Youp Kwak, <[e-mail]>

See Also

getprofile

Examples

data(simspal)
simspal <- calc.genoprob(simspal, step=0)


phe <- 1:nphe(simspal)


# difference between tpy = "sep" and "comb"

par(mfrow=c(1,2))
qtlslod <- makeqtl(simspal, chr = c(1, 1, 4),
               pos = c(36.6, 61, 27.8), what = "prob")
lodmat1 <- getprofile(simspal, qtl =  qtlslod, pheno.cols =phe,
                    formula = y~Q1 + Q2 + Q3 , method = "hk", tpy = "sep")
plotprofile(lodmat1, main="tpy=\"sep\"")

lodmat2 <- getprofile(simspal, qtl =  qtlslod, pheno.cols =phe,
                    formula = y~Q1 + Q2 + Q3 , method = "hk", tpy = "comb")
plotprofile(lodmat2, main="tpy=\"comb\"")

ikwak2/funqtl documentation built on April 20, 2022, 3:58 a.m.