I've been trying to use the prepareGenomePlot for mouse data. However, I don't seem to fully understand why I am not getting the cytobands for the mouse genome. I used a small script as seen in this link link text
Which I modified like this:
# prepareGenomePlot example library(quantsmooth) # construct genomic positions CHR<-sample(19,40,replace=TRUE) # Chromosomes MapInfo<-lengthChromosome(CHR,"bases")*runif(length(CHR)) # position on chromosome chrompos<-prepareGenomePlot(data.frame(CHR,MapInfo),paintCytobands = TRUE, organism="mmu") # Chrompos returns a matrix with the positions of the elements on the plot # You can use all kinds of base graphics functions to annotate the chromosomes points(chrompos[,2],chrompos[,1]+0.1,pch="x",col="red") # Show connection between 3rd and 4th element segments(chrompos[3,2],chrompos[3,1],chrompos[4,2],chrompos[4,1],col="blue",lwd=2)
However I get a horrible graph like this link text with no cytogenetic bands info, and the chromosome sizes are also wrong. What I want to do is basically plot specific points on each of the mouse chromosomes with their cyto bands.
Any help will be much appreciated!!!