lmPanel: For overlaying the line from the copy number model over...

In rscharpf/crlmmCompendium: This package contains the compendium for copy number estimation with the crlmm package

Description

For overlaying the line from the copy number model over boxplots of the genotype cluster intensities (intensity scale)

Usage

lmPanel(..., line.col = "grey30", label.cex = 0.8, Ns, allele = "A", nu, ph, subscripts, ltext.y = 2500)

Arguments

...	passed to panel.bwplot
line.col	color of line segment
label.cex	size of font for plotting the number of samples for each genotype
Ns	The number of samples for each genotype
allele	which allele – must be 'A' or 'B'
nu	the intercept from the linear model
ph	the slope from the linear model
subscripts	ignored
ltext.y	height to plot the genotype frequencies

Value

nothing

Author(s)

R. Scharpf

See Also

panel.bwplot

Examples

library("crlmm")
library("crlmmCompendium")


###################################################
### chunk number 27: loadObject-exampleData1
###################################################
#line 1164 "manuscript.Rnw"
data(exampleData1)


###################################################
### chunk number 28: dataCnFigs
###################################################
#line 1175 "manuscript.Rnw"
a <- t(as.matrix(A(exampleData1)))
gt <- t(as.matrix(calls(exampleData1)))
nuA <- as.numeric(nu(exampleData1, "A"))
phA <- as.numeric(phi(exampleData1, "A"))
col <- brewer.pal(7, "Accent")[c(1, 4, 7)]
NN <- Ns(exampleData1, i=1:16, j=1)[, , 1]
fns <- featureNames(exampleData1)
snpId <- matrix(fns, nrow(a), ncol(a), byrow=TRUE)
snpId <- factor(snpId, levels=fns, ordered=TRUE)  ##IMPORTANT
ldat <- data.frame(A=as.integer(a),
		   gt=as.factor(c("AA", "AB", "BB")[as.integer(gt)]),
		   snp=snpId)
(fig <- bwplot(A~gt|snp, ldat, cex=0.6, panel=lmPanel, nu=nuA, ph=phA,
	      fill="lightblue", Ns=NN,
	      par.strip.text=list(lines=0.9, cex=0.6), ylab=expression(I[A]), ltext.y=2500))


###################################################
### chunk number 29: boxplotA
###################################################
#line 1193 "manuscript.Rnw"
pars <- trellis.par.get()
pars$axis.text$cex <- 0.3
pars$xlab.text$cex <- 0.8
trellis.par.set("axis.text", pars$axis.text)
trellis.par.set("axis.text", pars$xlab.text)
print(fig)

rscharpf/crlmmCompendium documentation built on May 28, 2019, 3:31 a.m.