LDheatmap.addScatterplot

Add a scatter plot to an LDheatmap object

Add a scatter plot to an LDheatmap object. The x axis is the map of genetic distances of the SNPs.

Usage

LDheatmap.addScatterplot(LDheatmap, P, height = 0.2, ylab = NULL, ylim=NULL,
type = "points")

Details

The function creates an "association" grob and adds it to the LDheatmap object. Then it pushes a viewport and draws the LDheatmapGrob onto it.

Note

The function can display at most two scatter plots in the default setting. To add three or more scatter plots in the same viewport, the user can change the input value "location" from function constructVP which is the function inside the LDheatmap.addScatterplot. The default "location" value is 0.03, for adding the third scatter plot, user needs to set the "location" to 0.23, where 0.2 units is the height of the scatter plot. For the fourth scatter plot, set the "location" to 0.43 etc. See Examples for usage.

See Also

LDheatmap

Aliases

• LDheatmap.addScatterplot

Examples

# NOT RUN {
# Load the package's data set
data("CEUData")
# Produce an LDheatmap object
MyLDheatmap <- LDheatmap(CEUSNP, genetic.distances = CEUDist, flip = TRUE)
# Generate an arbitrary vector of values to plot
Yvalues <- seq(length = length(MyLDheatmap$genetic.distances), from = 0.01, to = 0.5)
# Add scatter plot
assoc <- LDheatmap.addScatterplot(MyLDheatmap, Yvalues)
######## Adding three or more scatter plots ########
# Redefine LDheatmap.addScatterplot() to display the third scatter plot
LDheatmap.addScatterplot_test3 <- function(LDheatmap, P, height=0.2, ylab=NULL, 
ylim=NULL, type="points",color,pch) {
if (dim(LDheatmap$LDmatrix)[1] != length(P)) {
print("Length of vector not equal number of SNPs in LDheatmap")
return()

flip <- !is.null(LDheatmap$flipVP)
vp <- constructVP(LDheatmap$LDheatmapGrob, 0.23, flip)
......
return(LDheatmap)
}}
environment(LDheatmap.addScatterplot_test3) <- asNamespace('LDheatmap')

# }