change color for cmplot

[asaki1986]

Hi all,

It is very helpful using CMplot to plot SNP effect, using script as follows,

CMplot(cattle50K, type="h",plot.type="m", band=0.5, LOG10=FALSE, ylab="SNP effect",ylim=c(-0.02,0.02), threshold.lty=2, threshold.lwd=1, threshold.col="red", amplify=FALSE,cex=0.6, chr.den.col=NULL, file="jpg",file.name="",dpi=300,file.output=TRUE,verbose=TRUE)

It will be great if anyone know how to change the script to display snp effect >0 as blue, while <0 as red.

Best,
Junfeng

[YinLiLin]

It can be achieved by using the arguments 'threshold' and 'signal.col':

1. transform the format of example data as the same with yours:

cattle50K[,4:ncol(cattle50K)] <- apply(cattle50K[,4:ncol(cattle50K)], 2, function(x) x*sample(c(1,-1), length(x), rep=TRUE))

2. generate the plot as you desired:

CMplot(cattle50K,plot.type="m",threshold=c(-10,0),signal.col=c("blue","red"),LOG10=F)
Note that the lower boundary '-10' can be any value but should be smaller than the minimum one in your data.