LDheatmap.addScatterplot: Add a scatter plot to an LDheatmap object

In LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

Add a scatter plot to an LDheatmap object

Description

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")

Arguments

LDheatmap	An object of class LDheatmap.
P	A vector with the values to be plotted as the y axis.
height	The height of the plot.
ylab	The y axis label.
ylim	The y axis limits.
type	Plot type. Possible values are "points" (the default), "lines" or "both".

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.

Value

An object of class LDheatmap given as an argument, with the grob LDheatmapGrob modified to inclue the "association" child grob.

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.

Author(s)

Sigal Blay <[e-mail]> and more

See Also

LDheatmap

Examples

# Load the package's data set
data("CEUSNP"); data("CEUDist")
# 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')

LDheatmap documentation built on April 24, 2022, 1:05 a.m.