LDheatmap.marks {LDheatmap} | R Documentation |
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(...), ...)
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 onto gpar
function. |
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^k,
j^k)-th cells (for k=1,...K; K =
length of the vectors i
and j
), where
i^k and
j^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))
.
x |
The vector of x coordinate(s) of the plotted symbol(s). |
y |
The vector of y coordinate(s) of the plotted symbol(s). |
Nicholas Lewin-Koh <nikko@hailmail.net>
data(LDheatmapData) tt <- LDheatmap(HapMap.dat, genetic.distances=distance) LDheatmap.marks(tt, 15, 3, cex=1.6, col="blue")