LDheatmap.highlight {LDheatmap} | R Documentation |
The function LDheatmap.highlight
is used to highlight a
specified genetic region in the linkage disequilibrium (LD)
heat map drawn with the LDheatmap
function.
LDheatmap.highlight(LDheatmap, i, j, fill = "NA", col = "black", lwd = 1, lty = 1)
LDheatmap |
An object of class "LDheatmap" (returned
by the function LDheatmap ). |
i |
A numeric value specifying the index of the first SNP to be in the highlighted region. |
j |
A numeric value specifying the index of the last SNP,
which must be different from i , to be in the highlighted region. |
fill |
Color to fill the highlighted area with. |
col |
A character string specifying the color of the line
segments defining the boundary of highlighted region; see
par . |
lwd |
A positive number specifying the width of the boundary segments. |
lty |
Either an integer or a character string specifying the
line type of the boundary segments; see par
for possible values. |
A data frame of the x and y coordinates of points defining the border of the highlighted area.
The function LDheatmap.highlight
highlights the cells representing
the pairwise LD for the SNPs located between i
-th and j
-th (inclusive)
SNPs in the genomic region of interest.
Note that the order of indices has no effect on the plot. For example,
LDheatmap.highlight(LDheatmap, i=2, j=4)
is the same as
LDheatmap.highlight(LDheatmap, i=4, j=2)
, which highlights
the cells representing the pairwise LD for the second,
third and fourth SNPs.
Nicholas Lewin-Koh <nikko@hailmail.net>, Ji-hyung Shin <jshinb@sfu.ca>, Sigal Blay <sblay@sfu.ca>
data(LDheatmapData) tt <- LDheatmap(HapMap.dat, genetic.distances=distance) LDheatmap.highlight(tt, 3, 8, col="blue", fill="green", lwd=3)