plot.LDblocks {trio} | R Documentation |
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.
## 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, ...)
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 .
|
Holger Schwender, holger.schwender@udo.edu
Gabriel, S.B. et al.~(2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 2225-2229.
## 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)