[BioC] Plotting question: how to plot SNP location data?

[Thomas Girke]

Hi Lauri,
I am often using the following featurePlot() function for similar purposes:
source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt") 

The instructions that are printed to the screen, after the sourcing step, should explain 
its usage. To color features (SNPs) in different colors, you simply provide under the 
featurecol argument a vector of numbers or color names.

Thomas

On Tue 10/30/07 14:54, Lauri.Nikkinen at veripalvelu.fi wrote:
> Hello,
> 
> I would like to plot specific SNPs with their exact locations on a
> chromosome. Based on my genotyping results I would like to separate
> these SNPs in three different categories: 1, 2 and 3 and use different
> colours to represent these categories. The script below generates the
> sample data. I can plot these with the image function using the
> following:
> 
> val <- 1:3
> samp <- sample(val, 100, replace=TRUE)
> z <- matrix(samp, nrow=20, ncol=4, byrow=TRUE)
> SNP <- 1:20
> siblings <- 1:4
> 
> opar <- par(cex=0.7)
> image(SNP, siblings, z, col=c("blue", "red", "black"), axes=FALSE,
> ann=FALSE)
> axis(1, at=1:20, labels=paste(rep("SNP", 20), 1:20), las=2)
> axis(2, at=1:4)
> mtext("sibling", 2, line=3)
> title(main="Specific SNPs in Chr 1")
> par(opar)
> 
> In addition to having the data for the above colour matrix, I also have
> data including the exact locations of the SNPs on a chromosome (snploc).
> I would like to plot the SPNs using the colour codes from above (z) and
> include the exact locations of each SNP. Is it possible to do that using
> the image-function? Below I have tried to solve the problem using the
> basic plot function but I cannot include the colors to that plot. How
> would that be possible?
> 
> colnames(z) <- c("sib1","sib2","sib3","sib4")
> rownames(z) <- paste(rep("SNP", 20), 1:20)
> z.t <- t(z)
> 
> #snploc$location represents the location of the SNP in the chromosome
> snploc <- data.frame(SNP=paste(rep("SNP", 20), 1:20),
> location=c(4.2,5.8,6.9,3,8,7,5,4,3.6,4.3,4.6,6.6,5.2,6,9,9.4,12,16,14,12
> .3))
> snploc$SNP <- factor(snploc$SNP, levels=unique(snploc$SNP))
> temp <- as.data.frame(sapply(levels(snploc$SNP), function(x){   z.t[,x]
> <- snploc$location[snploc$SNP == x];
>  
> z.t[,x]
>  
> }))
> 
> 
> temp1 <- as.list(temp)
> #Plot the location of the SNP
> x11()
> for (i in names(temp1)) {
>           opar <- par(new=TRUE)
>           plot(temp1[[i]], 1:4, pch="|", ann=FALSE, col="blue",
> xlim=c(0, 20), ylim=c(1,4), yaxp=c(1,4,3))
>           par(opar)
>           }
> mtext("SNP location", 1, line=3)
> mtext("sibling", 2, line=3)
> opar <- par(cex=0.7)
> axis(3, at=snploc$location, labels=snploc$SNP, las=3)
> par(opar)
> 
> Originally my z.t data.frame has dimensios 33*4000 so looping through
> this data.frame is tedious.
> 
> Thanks, 
> Lauri
> 
> ***************************
> Lauri Nikkinen
> Finnish Red Cross Blood Service
> www.bloodservice.fi
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437