Question: Plot Positions On Chromosomes
1
gravatar for Nicolas Rosewick
4.0 years ago by
Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
Nicolas Rosewick5.3k wrote:

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.

enter image description here

plot position chromosome • 3.5k views
ADD COMMENTlink modified 4.0 years ago by Irsan6.3k • written 4.0 years ago by Nicolas Rosewick5.3k

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

ADD REPLYlink written 24 days ago by steve880
2
gravatar for Sean Davis
4.0 years ago by
Sean Davis23k
National Institutes of Health, Bethesda, MD
Sean Davis23k wrote:

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

ADD COMMENTlink written 4.0 years ago by Sean Davis23k
2
gravatar for Irsan
4.0 years ago by
Irsan6.3k
Amsterdam
Irsan6.3k wrote:
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))

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Irsan6.3k
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