Description Usage Arguments Value Author(s) See Also Examples
For overlaying the line from the copy number model over boxplots of the genotype cluster intensities (intensity scale)
1 |
... |
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 |
nothing
R. Scharpf
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | 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)
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