Plots a symbol in the centers of cells of the heat map image

The function LDheatmap.marks() is used to plot a symbol in the centers of cells representing the pairwise linkage disequilibria of specified pairs of SNPs.

LDheatmap.marks(LDheatmap, i, j = NULL, pch = 20, gp=gpar(...), ...)

Arguments

LDheatmap

An object of class "LDheatmap" returned by the function LDheatmap().
i

A vector of indices of the first set of SNPs.
j

A vector of indices of the second set of SNPs.
pch

Either an integer value or a single character specifying the symbol to be plotted. See points() for possible values and their corresponding symbols.
gp

Graphical parameters; See gpar().
...

Graphical parameter settings to be passed on to the gpar() function.

Value

x

The vector of x coordinate(s) of the plotted symbol(s).

y

The vector of y coordinate(s) of the plotted symbol(s).

Details

The lengths of the vectors i and j must be the same and greater than or equal to 1. If the lengths are greater than 1, the function plots the specified symbol in the centers of the (i\(\mbox{\textasciicircum}\)k, j\(\mbox{\textasciicircum}\)k)-th cells (for k=1,...K; K = length of the vectors i and j), where i\(\mbox{\textasciicircum}\)k and j\(\mbox{\textasciicircum}\)k are the k-th elements of vectors i and j, respectively. For example, if i=c(1,2) and j=c(3,5), LDheatmap() plots a symbol in the centers of the cells representing pairwise linkage disequilibria between the first and third SNPs and between the second and fifth SNPs in the genome of interest. Note that the order of the sets of indices does not matter; for example, LDheatmap.marks(LDheatmap, i=c(1,2), j=c(3,5)) is equivalent to LDheatmap.marks(LDheatmap, i=c(3,5), j=c(1,2)).

Warning

By default, LDheatmap.marks() finds the viewport to draw on from the LDheatmap object passed to it as an argument. However, if LDheatmap() was called with the option pop=TRUE, the resulting LDheatmap object is not assigned a viewport. In this case, LDheatmap.marks() assumes the user wishes to highlight in the current viewport. Therefore, if LDheatmap() has been called with the option pop=TRUE, the user must navigate to the correct viewport before calling LDheatmap.marks().

Examples

data(CEUData)
tt <- LDheatmap(CEUSNP, genetic.distances=CEUDist)
LDheatmap.marks(tt, 15, 3, cex=1.6, col="blue")