R: Plot genetic markers in additive log-ratio coordinates
HWAlrPlot
R Documentation
Plot genetic markers in additive log-ratio coordinates
Description
HWAlrPlot creates a scatter plot of the log-ratio coordinates of
bi-allelic genetic markers. Hardy-Weinberg equilibrium is indicated by
a straigh line in the plot.
Usage
HWAlrPlot(X, zeroadj = 0.5)
Arguments
X
A matrix of genotype counts (columns AA, AB, BB)
zeroadj
Zero-adjustment parameter. Zero counts in the count
matrix are substituted by zeroadj which is 0.5 by default.
Value
NULL
Author(s)
Jan Graffelman (jan.graffelman@upc.edu)
References
Graffelman, J. and Egozcue, J. J. (2011) Hardy-Weinberg
equilibrium: a non-parametric compositional approach. In: Vera
Pawlowsky-Glahn and Antonella Buccianti (eds.) Compositional Data
Analysis: Theory and Applications, John Wiley & Sons, Ltd, pp. 207-215
See Also
HWClrPlot,HWIlrPlot
Examples
X <- HWClo(HWData(100,100))
HWAlrPlot(X)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(HardyWeinberg)
Loading required package: mice
Loading required package: Rcpp
mice 2.25 2015-11-09
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HardyWeinberg/HWAlrPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HWAlrPlot
> ### Title: Plot genetic markers in additive log-ratio coordinates
> ### Aliases: HWAlrPlot
> ### Keywords: aplot
>
> ### ** Examples
>
> X <- HWClo(HWData(100,100))
> HWAlrPlot(X)
NULL
>
>
>
>
>
> dev.off()
null device
1
>