plotlod: Plot signed or plain LOD image.

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

Plot signed or plain LOD image.

Description

Plot signed or plain LOD image. (taking -LOD when the QTL effect is negative), where (i,j) element is for phenotype i at marker j.

Usage

plotlod(
  output,
  effects,
  y,
  ylab = "Time",
  gap = 25,
  ncolors = 251,
  horizontal = FALSE,
  ...
)

Arguments

output	An object of class "scanone" as produced by scanone.
effects	The sign information whether the QTL having AA do negative effect. Get this by using geteffects.
y	Positions of phenotypes in image (e.g., the times).
ylab	y-axis label
gap	The gap between chromosomes.
ncolors	The number of colors between blue and red.
horizontal	If TRUE, transpose the x and y axes
...	More graphical components, passed image.plot.

Value

None.

Author(s)

Karl W Broman, Il-Youp Kwak, <email: [e-mail]>

See Also

geteffects

Examples

data(simspal)
simspal <- calc.genoprob(simspal)
phe <- 1:nphe(simspal)

out <- scanone(simspal, pheno.col=phe, method="hk")
eff <- geteffects(simspal, pheno.cols=phe)
nam <- phenames(simspal)
y <- as.numeric(substr(nam, 2, nchar(nam)))/60

plotlod(out, eff, y,  gap=15)
plotlod(out, y=y, gap=15, horizontal = TRUE)

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