# LDheatmap.highlight

0th

Percentile

##### Highlight a genetic region in the linkage disequilibrium heat map

The function LDheatmap.highlight() is used to highlight a specified genetic region in the linkage disequilibrium (LD) heat map drawn with the LDheatmap() function.

Keywords
aplot
##### Usage
LDheatmap.highlight(LDheatmap, i, j, fill = "NA", col = "black", lwd = 1,
lty = 1,flipOutline=FALSE, crissCross = FALSE)
##### Arguments
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() for possible values.

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.

flipOutline

A Boolean variable that flips the outlined section over the diagonal of the heatmap.

crissCross

A Boolean variable that controls whether a contiguous selection of SNPs are outlined only on their polygonal boundary or at individual SNP levels.

##### Value

A data frame of the x and y coordinates of points defining the border of the highlighted area.

##### Note

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. 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.

##### Warning

By default, LDheatmap.highlight() 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.highlight() 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.highlight().

##### Aliases
• LDheatmap.highlight
##### Examples
# NOT RUN {
data(CEUData)
tt <- LDheatmap(CEUSNP, genetic.distances=CEUDist)
LDheatmap.highlight(tt, 3, 8, col="blue", fill="green", lwd=3, flipOutline=FALSE, crissCross=FALSE)
# }

Documentation reproduced from package LDheatmap, version 0.99-7, License: GPL-3

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