> install.packages("CMplot")
> library("CMplot")

# if you want to use the latest version:
> source("https://raw.githubusercontent.com/YinLiLin/R-CMplot/master/R/CMplot.r")

> data(pig60K)   #calculated p-values by MLM
> data(cattle50K)   #calculated SNP effects by rrblup
> head(pig60K)

          SNP Chromosome Position    trait1     trait2     trait3
1 ALGA0000009          1    52297 0.7738187 0.51194318 0.51194318
2 ALGA0000014          1    79763 0.7738187 0.51194318 0.51194318
3 ALGA0000021          1   209568 0.7583016 0.98405289 0.98405289
4 ALGA0000022          1   292758 0.7200305 0.48887140 0.48887140
5 ALGA0000046          1   747831 0.9736840 0.22096836 0.22096836
6 ALGA0000047          1   761957 0.9174565 0.05753712 0.05753712

> head(cattle50K)

   SNP chr    pos Somatic cell score  Milk yield Fat percentage
1 SNP1   1  59082        0.000244361 0.000484255    0.001379210
2 SNP2   1 118164        0.000532272 0.000039800    0.000598951
3 SNP3   1 177246        0.001633058 0.000311645    0.000279427
4 SNP4   1 236328        0.001412865 0.000909370    0.001040161
5 SNP5   1 295410        0.000090700 0.002202973    0.000351394
6 SNP6   1 354493        0.000110681 0.000342628    0.000105792

> CMplot(pig60K,plot.type="d",bin.size=1e6,chr.den.col=c("darkgreen", "yellow", "red"),file="jpg",memo="",dpi=300,
    file.output=TRUE,verbose=TRUE,width=9,height=6)
# users can personally set the windowsize and the min/max of legend by:
# bin.size=1e6
# bin.range=c(min, max)
# memo: add a character to the output file name
# chr.labels: change the chromosome names

> CMplot(pig60K,plot.type="c",chr.labels=paste("Chr",c(1:18,"X"),sep=""),r=0.4,cir.legend=TRUE,
        outward=FALSE,cir.legend.col="black",cir.chr.h=1.3,chr.den.col="black",file="jpg",
        memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=10,height=10)

> CMplot(pig60K,plot.type="c",r=0.4,col=c("grey30","grey60"),chr.labels=paste("Chr",c(1:18,"X"),sep=""),
      threshold=c(1e-6,1e-4),cir.chr.h=1.5,amplify=TRUE,threshold.lty=c(1,2),threshold.col=c("red",
      "blue"),signal.line=1,signal.col=c("red","green"),chr.den.col=c("darkgreen","yellow","red"),
      bin.size=1e6,outward=FALSE,file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=10,height=10)

#Note:
1. if signal.line=NULL, the lines that crosse circles won't be added.
2. if the length of parameter 'chr.den.col' is not equal to 1, SNP density that counts 
   the number of SNP within given size('bin.size') will be plotted around the circle.

> CMplot(cattle50K,plot.type="c",LOG10=FALSE,outward=TRUE,col=matrix(c("#4DAF4A",NA,NA,"dodgerblue4",
         "deepskyblue",NA,"dodgerblue1", "olivedrab3", "darkgoldenrod1"), nrow=3, byrow=TRUE),
         chr.labels=paste("Chr",c(1:29),sep=""),threshold=NULL,r=1.2,cir.chr.h=1.5,cir.legend.cex=0.5,
         cir.band=1,file="jpg", memo="",dpi=300,chr.den.col="black",file.output=TRUE,verbose=TRUE,
         width=10,height=10)
        
#Note: parameter 'col' can be either vector or matrix, if a matrix, each trait can be plotted in different colors.

> CMplot(pig60K,plot.type="m",LOG10=TRUE,threshold=NULL,file="jpg",memo="",dpi=300,
    file.output=TRUE,verbose=TRUE,width=14,height=6)

> CMplot(pig60K, plot.type="m", col=c("grey30","grey60"), LOG10=TRUE, ylim=c(2,12), threshold=c(1e-6,1e-4),
        threshold.lty=c(1,2), threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,
        chr.den.col=NULL, signal.col=c("red","green"), signal.cex=c(1,1),signal.pch=c(19,19),
        file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)

#Note: if the ylim is setted, then CMplot will only plot the ponits which among this interval.

> CMplot(pig60K, plot.type="m", LOG10=TRUE, ylim=NULL, threshold=c(1e-6,1e-4),threshold.lty=c(1,2),
        threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,bin.size=1e6,
        chr.den.col=c("darkgreen", "yellow", "red"),signal.col=c("red","green"),signal.cex=c(1,1),
        signal.pch=c(19,19),file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,
        width=14,height=6)
        
#Note: if the length of parameter 'chr.den.col' is bigger than 1, SNP density that counts 
   the number of SNP within given size('bin.size') will be plotted.

> signal <- pig60K$Position[which.min(pig60K$trait2)]
> SNPs <- pig60K$SNP[pig60K$Chromosome==13 & 
        pig60K$Position<(signal+1000000)&pig60K$Position>(signal-1000000)]
> CMplot(pig60K, plot.type="m",LOG10=TRUE,col=c("grey30","grey60"),highlight=SNPs,
        highlight.col="green",highlight.cex=1,highlight.pch=19,file="jpg",memo="",
        dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
#Note:
highlight.col, highlight.cex, highlight.pch can be value or vecter, if its length equals to the length of highlighted SNPs,
each SNPs have its special colour, size and shape.

> CMplot(pig60K[pig60K$Chromosome==13, ], plot.type="m",LOG10=TRUE,col=c("grey60"),highlight=SNPs,
        highlight.col="green",highlight.cex=1,highlight.pch=19,file="jpg",memo="", 
        threshold=c(1e-6,1e-4),threshold.lty=c(1,2),threshold.lwd=c(1,2), width=9,height=6,
        threshold.col=c("red","blue"),amplify=FALSE,dpi=300,file.output=TRUE,verbose=TRUE)

> SNPs <- pig60K[pig60K[,5] < (0.05 / nrow(pig60K)), 1]
> genes <- paste("GENE", 1:length(SNPs), sep="_")
> set.seed(666666)
> CMplot(pig60K[,c(1:3,5)], plot.type="m",LOG10=TRUE,col=c("grey30","grey60"),highlight=SNPs,
        highlight.col=c("red","blue","green"),highlight.cex=1,highlight.pch=c(15:17), highlight.text=genes,      
        highlight.text.col=c("red","blue","green"),threshold=0.05/nrow(pig60K),threshold.lty=2,   
        amplify=FALSE,file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
#Note:
the order of 'highlight.text' must be consistent with 'highlight'
highlight.text.cex: value or vecter, control the size of added text
highlight.text.font: value or vecter, control the font of added text
highlight.text.xadj: value or vecter, -1, 0, 1 limited, control the position of text around the highlighted SNPs,
                     -1(left), 0(center), 1(right)
highlight.text.yadj: value or vecter, same as above, -1(down), 0(center), 1(up)

> CMplot(cattle50K, plot.type="m", band=0.5, LOG10=FALSE, ylab="SNP effect",threshold=0.015,
        threshold.lty=2, threshold.lwd=1, threshold.col="red", amplify=TRUE, width=14,height=6,
        signal.col=NULL, chr.den.col=NULL, file="jpg",memo="",dpi=300,file.output=TRUE,
        verbose=TRUE,cex=0.8)
#Note: if signal.col=NULL, the significant SNPs will be plotted with original colors.

> cattle50K[,4:ncol(cattle50K)] <- apply(cattle50K[,4:ncol(cattle50K)], 2, 
         function(x) x*sample(c(1,-1), length(x), rep=TRUE))
> CMplot(cattle50K, plot.type="m", band=0, 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",memo="",dpi=300,file.output=TRUE,verbose=TRUE)

#Note: Positive and negative values are acceptable.

> CMplot(pig60K, plot.type="m",pch=1:3,multracks=TRUE,threshold=c(1e-6,1e-4),threshold.lty=c(1,2), 
        threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,bin.size=1e6,
        chr.den.col=c("darkgreen", "yellow", "red"), signal.col=c("red","green"),signal.cex=c(1,1),
        file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE)

> CMplot(pig60K,plot.type="q",conf.int=TRUE,box=FALSE,file="jpg",memo="",dpi=300,
    ,file.output=TRUE,verbose=TRUE,width=5,height=5)

> pig60K$trait1[sample(1:nrow(pig60K), round(nrow(pig60K)*0.80))] <- NA
> pig60K$trait2[sample(1:nrow(pig60K), round(nrow(pig60K)*0.25))] <- NA
> CMplot(pig60K,plot.type="q",col=c("dodgerblue1", "olivedrab3", "darkgoldenrod1"),threshold=1e-6,
        signal.pch=19,signal.cex=1.5,signal.col="red",conf.int=TRUE,box=FALSE,multracks=
        TRUE,file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,ylim=c(0,8),width=5,height=5)