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Last data update: 2014.03.03

R: Scatter plot of the genotype frequencies

HWGenotypePlot

R Documentation

Scatter plot of the genotype frequencies

Description

HWGenotypePlot makes a scatterplots of the AB or BB frequency versus the AA frequency and represents a blue curve indicating the Hardy-Weinberg equilibrium condition.

Usage

HWGenotypePlot(X, plottype = 1, xlab = expression(f[AA]), ylab =
ifelse(plottype == 1, expression(f[AB]), expression(f[BB])), asp = 1,
pch = 19, xlim = c(0, 1), ylim = c(0, 1), cex = 1, cex.axis = 2, cex.lab = 2, ...)

Arguments

`X`	A matrix of genotype counts or frequencies with three columns (AA, AB, BB)
`plottype`	`plottype=1` produces a plot of AB versus AA, `plottype=2` produced a plot of BB versus AA.
`xlab`	A label for the x axis
`ylab`	A label for the y axis
`asp`	Aspec ratio (1 by default)
`pch`	Plotting charachter (19 by default)
`xlim`	Limits for the x axis (0-1 by default)
`ylim`	Limits for the y axis (0-1 by default)
`cex`	Character expansion factor (1 by default)
`cex.axis`	Character expansion factor for the axes (2 by default)
`cex.lab`	Character expansion factor for labels of axis (2 by default)
`...`	Additional arguments for the `plot` function

Value

NULL

Author(s)

Jan Graffelman jan.graffelman@upc.edu

Examples

n <- 100 # sample size
m <- 100 # number of markers
Xc <- HWClo(HWData(n,m))
HWGenotypePlot(Xc,plottype=1,main="Heterozygote-homozygote scatterplot")

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/HWGenotypePlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HWGenotypePlot
> ### Title: Scatter plot of the genotype frequencies
> ### Aliases: HWGenotypePlot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> n <- 100 # sample size
> m <- 100 # number of markers
> Xc <- HWClo(HWData(n,m))
> HWGenotypePlot(Xc,plottype=1,main="Heterozygote-homozygote scatterplot")
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>