plotsignal: Plot Localized Admixture Signals

In adwave: Wavelet Analysis of Genomic Data from Admixed Populations

Description

Plotting function for objects of class adsig.

Usage

plotsignal(x, ind = NULL, popA = NULL, popB = NULL, xlab = NULL, ylab = NULL, 
		ylim = NULL, main = NULL)

Arguments

x	object of class adsig for plotting.
ind	character giving ID of a single individual to plot.
popA	(optional) name of ancestral population 1.
popB	(optional) name of ancestral population 2.
xlab	(optional) character string for x axis label.
ylab	(optional) character string for y axis label.
ylim	(optional) vector giving plotting range for y axis.
main	(optional) character string for title.

Value

Produces figure.

Author(s)

Jean Sanderson

References

Sanderson J, H Sudoyo, TM Karafet, MF Hammer and MP Cox. 2015. Reconstructing past admixture processes from local genomic ancestry using wavelet transformation. Genetics 200:469-481. https://doi.org/10.1534/genetics.115.176842

See Also

signal

Examples

data(admix)

# Generate the admixture signal with windowing
AdexPCA2 <- signal(admix$data,popA="popA",popB="popB",populations=admix$populations,
		tol=0.001,n.signal=1000,window.size=0.01)

# Plot resulting admixture signal for one individual
plotsignal(AdexPCA2,ind="AD00001",popA=AdexPCA2$popA,popB=AdexPCA2$popB)

Example output

Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5.1)

Number of individuals:	 50 
Number of individuals for finding axes:	 30 
Number of SNPs:		 3000 
Finished calculations 

adwave documentation built on May 1, 2019, 8 p.m.