Hi Einat

As Mehmet suggested, you can try plotGrandlinear in ggbio. an example codes
in the manual are here
http://tengfei.github.com/ggbio/docs/man/plotGrandLinear.html
how to install
http://www.bioconductor.org/packages/2.11/bioc/html/ggbio.html

But one thing is confusing(Maybe I don't get it right what you want), in
Manhattan plot, the x-axis shows chromosome names like in those example,
even though you have a short list with only 200 SNPs, if you hope to show
gene names as x-axis, that's going to be tricky

1. 200(suppose each snp fall in different genes) x-axis labels in a row is
hard or imporssible to read in the plot.
2. it's spread over multiple chromosomes, even if you really want to labels
them with gene names, it's tricky to do in gglot2 level.

IMHO, as a Manhattan overview, you don't have to show all the details like
gene names, just to check general distribution and outliers.

I guess what you want is probably a gene-list view like in IGV?

http://www.broadinstitute.org/igv/gene_list_view

suppose your 200 SNPs falls only to a few genes, let's say 10 genes. you
may want something like each gene take one facet or panel in a row/grid of
plots, would you mind to explain your case? or maybe you can shoot me
personal email for collaboration on your case, because complex gene-slit
views are not fully supported in ggbio yet.

Thanks

Tengfei


On Tue, Jan 8, 2013 at 1:19 PM, Suzen, Mehmet <msuzen@gmail.com> wrote:

> Hello Einat,
>
> Have you tried ggbio package's plotGrandLinear from bioconductor?
>
> Best,
> -m
>
> On 8 January 2013 20:03, Einat Granot <einatgranot@gmail.com> wrote:
> > Hello,
> > I am trying to create a simple Manhattan plot for a small list of 200
> SNPs
> > spread out in the genome in  different genes.
> > I have tried different functions (using ggplot2 and a function created by
> > Stephen Turner, mhtplot etc.)-none of them work smoothly.
> > Does anyone have a simple way to create the plot (not for all 22
> > chromosomes)- with the x axis showing the genes name and not the
> chromosomal
> > location.
> > Thanks a lot,
> > Einat
> >
> >         [[alternative HTML version deleted]]
> >
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>
> ______________________________________________
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
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>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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