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

    # 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")

[Package trio version 3.22.0 Index]