Plot Positions On Chromosomes

Question

[Nicolas Rosewick]

Hi,

How can I plot positions on chromosomes using R. I put a little example to better explain. So I've a dataframe for each sample containing positions of interest :

Chr    Pos
1    100
1    300
2    30
10    1000
11    2000

And I want to plot that on chromosomes like that (Here there are 6 samples A,B,C,D,E and F). each point represent the position in the dataframe

Anyone can help me ?

Thanks

N.

[steve]

I've made a post here with an example on how to create a plot that might help with this

Answer 1

[Sean Davis]

Have a look at the geneplotter bioconductor package as well as the Gviz package. In particular, see section 6 of the vignette.

http://www.bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf

Answer 2

[Irsan]

library(ggplot2) 
ggplot(dataframe) + geom_histogram(aes(x=Start),binwidth=1e6) + facet_grid(Chr ~Sample)

You need a data frame with colums Chr, Start and Sample. If you just want to see points, change geom_histogram(...) for geom_point(aes(x=start, y=0))