Question: Bioconductor Quantsmooth Preparegenomeplot For Mouse Data
2
gravatar for Sakti
7.1 years ago by
Sakti20
Sakti20 wrote:

Hi!!

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!!!

genome mouse bioconductor graphs • 2.8k views
ADD COMMENTlink modified 7.1 years ago by Julien Textoris430 • written 7.1 years ago by Sakti20

do you get any warnings ou errors ?

ADD REPLYlink written 7.0 years ago by Julien Textoris430
0
gravatar for Julien Textoris
7.0 years ago by
Marseille, France
Julien Textoris430 wrote:

Dear Sakti,

I don't have the answer, but maybe a path to it !

I searched a lot because i was intersted in painting band also and did not understand why the bands were plotted for human and not for mouse ??

In fact, in the prepareGenomePlot function, the line testing the paintCytoBands option is the following :

if (paintCytobands && organism == "hsa") {

this means that when you use a different organism than hsa, this option is not condidered. And in this post, i found that the cytobands data are only loaded for human in quantsmooth. But I did not figured out how to load mouse data also !! Maybe if you look at the code of the prepareGenomePlot function, you may found out how to do the work for you ? I'll paste a real answer if I found one !

hope this will helps !

Julien

ADD COMMENTlink written 7.0 years ago by Julien Textoris430
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