plot.LDblocks {trio}R Documentation

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

## S3 method for class 'LDblocks':
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.

Author(s)

Holger Schwender, holger.schwender@udo.edu

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

## Not run: 
# Andrea's data
data(mat)

# LD blocks can be identified either by
out <- getLD(mat, addVarN=TRUE)
out2 <- findLDblocks(out)
out2

# or directly by
out3 <- findLDblocks(mat)

# Plot Gabriel's categories with LD blocks for all SNPs.
plot(out3)

# Plot Gabriel's categories starting with SNP 24 and 
# ending with SNP 60.
plot(out3,  start=24, end=60)

# Note that the SNPs ABI.354, ABI.355, and ABI.357
# form a LD-block. But since ABI.354 is not part of
# the plot, and thus the block is only shown partly
# in the plot, the vertical block border is missing.

# Now the same for D', but by using the SNP names
plot(out3, "Dprime", start="ABI.355", end="CRC.45")
## End(Not run)

[Package trio version 1.0.2 Index]