gaston (version 1.4.9)

LD.plot: Plot Linkage Disequilibrium

Description

Pretty plot of a Linkage Disequilibrium (LD) matrix

Usage

LD.plot(LD, snp.positions, max.dist = Inf, depth = nrow(LD),  graphical.par = list(mar = c(0,0,0,0)), cex.ld, cex.snp, polygon.par = list(border = "white"),  color.scheme = function(ld) rgb(1,1-abs(ld),1-abs(ld)), write.snp.id = TRUE, write.ld = function(ld) sprintf("%.2f", ld), draw.chr = TRUE, above.space = 1 + 2*write.snp.id + draw.chr,  below.space = 1, pdf.file, finalize.pdf = TRUE)

Arguments

LD

A symmetric LD matrix (such as produced by LD

snp.positions

A vector of SNP positions

max.dist

Maximal distance above which the LD is not plotted

depth

Maximal number of neighbouring SNPs for which the LD is plotted

graphical.par

A list of graphical parameters for function par

cex.ld

The magnification to be used for LD values (if missing, an ad-hoc value is computed)

cex.snp

The magnification to be used for SNPs ids (if missing, an ad-hoc value is computed)

polygon.par

A list of parameters for function polygon

color.scheme

A function to set the background color of a cell

write.snp.id

Logical. If TRUE, SNP ids will be displayed above the plot

write.ld

NULL, or a function which outputs the string used for displaying a LD value in a cell

draw.chr

Logical. If TRUE, a chromosome with SNP positions is sketched above the plot

above.space

Space above the plot (in user units = height of a cell)

below.space

Space below the plot (in user units = height of a cell)

pdf.file

The name of a pdf file in which to plot the LD matrix. If missing, current plot device will be used

finalize.pdf

Logical. If TRUE, dev.off() will be called to finalize the pdf file

Details

This function displays a LD plot similar to Haploview plots.

To add anotations to the plot, it is useful to know that each cell has width and height equal to one user unit, the first cell in the upper row being centered at coordinates (1.5, -0.5).

See Also

LD

Examples

# Load data
data(AGT)
x <- as.bed.matrix(AGT.gen, AGT.fam, AGT.bim)

# Compute LD
ld.x <- LD(x, c(1,ncol(x)))

# Plot a tiny part of the LD matrix
LD.plot( ld.x[1:20,1:20], snp.positions = x@snps$pos[1:20] )

# Customize the plot
LD.plot( ld.x[1:20,1:20], snp.positions = x@snps$pos[1:20], 
         graphical.par = list(cex = 1.3, bg = "gray"), 
         polygon.par = list(border = NA), write.ld = NULL )
## Not run: 
# # Plotting the whole matrix in X11 display is very long (lots of polygons)
# # but it is ok with a pdf file
# LD.plot(ld.x, snp.positions = x@snps$pos, max.dist = 50e3, write.ld = NULL, pdf.file = "LD_AGT.pdf")
# ## End(Not run)