Last data update: 2014.03.03

 R: function to plot additional GWAA results
add.plotR Documentation

function to plot additional GWAA results

Description

Add plot of results of GWA analysis

Usage

add.plot(x, ..., df = 1,  col=c("lightgreen","lightblue"), sort=TRUE, delta = 1)

Arguments

x

object of type scan.gwaa-class, as returned by scan.glm, qtscore, ccfast, emp.ccfast, emp.qtscore, or scan.haplo; or of type scan.gwaa.2D-class, as returned by scan.haplo.2D or scan.glm.2D.

...

additional arguments to be passed to plot

df

P-value at which df to add (1, 2 or "Pc1df")

col

which colors to use to depict consecutive chromosomes

sort

whether results should be plotted after sorting by chromosome and position

delta

gap width between chromosomes

Value

No value returned.

Author(s)

Yurii Aulchenko

See Also

plot, snp.subset, scan.glm, qtscore, ccfast, emp.qtscore, emp.ccfast, scan.haplo, scan.haplo.2D, scan.glm.2D

Examples

require(GenABEL.data)
data(srdta)
a <- ccfast("bt",srdta,snps=c(1:100))
plot(a)
a1 <- qtscore(bt,srdta,snps=c(1:100))
add.plot(a1,col="red",type="l")

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(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/add.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: add.plot
> ### Title: function to plot additional GWAA results
> ### Aliases: add.plot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> require(GenABEL.data)
> data(srdta)
> a <- ccfast("bt",srdta,snps=c(1:100))
Warning in ccfast("bt", srdta, snps = c(1:100)) :
  11 people (out of 2500 ) excluded as not having cc status

> plot(a)
> a1 <- qtscore(bt,srdta,snps=c(1:100))
Warning messages:
1: In test.type(y, trait.type) : binomial trait is analysed as gaussian
2: In qtscore(bt, srdta, snps = c(1:100)) :
  11 observations deleted due to missingness
3: In qtscore(bt, srdta, snps = c(1:100)) : Lambda estimated < 1, set to 1
> add.plot(a1,col="red",type="l")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO