trio (version 3.10.0)

plot.LDblocks: Plotting a LDblock Object

Description

Plots either the pairwise D' values or the pairwise LD categorization used in the procedure of Gabriel et al. (2002). Additionally, the LD blocks are marked in this plot.

Usage

"plot"(x, y = "gabriel", col = NULL, start = 1, end = NA, xlab = "", ylab = "", cexAxis = 0.8, block.col = 2, block.lwd = 3, ...)

Arguments

x

the output of findLDblocks.

y

either "Dprime" or "gabriel" (default) specifying the LD values that should be plotted.

col

a vector specifying the colors used in plotting of the LD values. If y = "Dprime", different levels of gray will be used by default (the darker, the higher is the LD value). If y = "gabriel", strong LD is by default marked by blue fields, evidence of recombination by white color, and others by yellow.

start

integer or character string specifying the index or name of the first SNP, respectively, that should be plotted, where the index corresponds to the column (or row if snp.in.col = FALSE) of the matrix used as input in getLD or findLDblocks.

end

integer or character string specifying the index or name of the last SNP, respectively, that should be plotted.

xlab

character string naming the label of the x-axis.

ylab

character string naming the label of the y-axis.

cexAxis

a numeric value specifying the relative size of the SNP names displayed at the axes of the plot.

block.col

the color of the lines used to show the borders of the LD blocks.

block.lwd

numeric value specifying the size of the lines used to show the borders of the LD blocks

...

further arguments of image.

References

Gabriel, S.B. et al.~(2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 2225-2229.

See Also

findLDblocks, plot.getLD

Examples

# Load the simulated data.
data(trio.data)

# Estimate LD blocks.
blocks <- findLDblocks(LDdata)

# Alternatively, the LD blocks can be estimated by
ld.out <- getLD(LDdata, addVarN=TRUE)
blocks2 <- findLDblocks(ld.out)

# Plot the LD blocks showing the Gabriel categorization.
plot(blocks)

# Plot the LD blocks showing the Dprime values.
plot(blocks, "Dprime")