[BioC] GenomeGraphs question

[Joern Toedling]

Hello,

the function "setPar" might be what you are looking for.

You can check the parameters associated with each object easily by just 
typing the object's name, such as
 > snpPlot

and set them this way:
 > setPar(snpPlot, "pointSize", 2) # or something else than 2

and then calling "gdPlot" will probably do the trick.

Regards,
Joern




On 02/08/2012 04:53 PM, Iain Gallagher wrote:
>
> Dear List
>
> I am plotting some snps using GenomeGraphs to show genomic context. I have a simple question: how do I change the size of the plotting character?
>
> # SCRIPT BEGINS
>
> require(biomaRt) # get and load the library
> require(GenomeGraphs)
>
> # get the snps we need info on
> snps<- c('rs136617760', 'rs42494357', 'rs110465273', 'rs42494342',  'rs109809949', 'rs134449285', 'rs137562332', 'rs132841890')
>
> # set up the database we need to query
> snpmart<- useMart('snp', dataset = 'btaurus_snp')
>
> # we want to get the snp id, allele, chromosome position and chromosome
> # in biomaRt attributes are what you want, filters are what you're using to query the db
> # there's load of info available; use listAttributes(snpmart) to see what you can get back
> # and listFilters(snpmart) to see what you can put in as a query
>
> snpInfo<- getBM(attributes = c('refsnp_id', 'allele', 'chrom_start', 'chr_name'), filters = 'snp_filter', values = snps, mart = snpmart)
>
> # plot these using GenomeGraphs
> # subset out the chromosome 13 snps
> thirteenSnps<- subset(snpInfo, snpInfo$chr_name == 13)
>
> # make pretend 'intensity values' for later
> ints<- seq(1,6) # could replace with 1/log10p perhaps!
> names(ints)<- thirteenSnps$refsnp_id
> ints<- as.matrix(ints)
>
> # set up mart
> cowmart<- useMart('ensembl', dataset = 'btaurus_gene_ensembl')
>
> # make a plot of the genes on bovine chromosome 13 around the SNPs Mairead found on chromosome 13
> ideogram<- makeIdeogram(chromosome = 13)
>
> plusStrand<- makeGeneRegion(chromosome = 13, start = min(thirteenSnps$chrom_start)-5e5, end = min(thirteenSnps$chrom_start)+5e5, strand = "+", biomart = cowmart)
>
> minStrand<- makeGeneRegion( chromosome = 13, start = min(thirteenSnps$chrom_start)-5e5, end = min(thirteenSnps$chrom_start)+5e5, strand = "-", biomart = cowmart)
>
> genomeAxis<- makeGenomeAxis(add53 = TRUE, add35 = TRUE)
>
> snpPlot<- makeGenericArray(intensity = ints, probeStart = thirteenSnps$chrom_start,  dp = DisplayPars(color="darkred", type="point", cex = 2))
>
> gdPlot(list(makeTitle('Chromosome 13'), a = ideogram, b = plusStrand, c = genomeAxis, d = minStrand, e = snpPlot), labelCex = 2, labelRot = 0)
>
> # SCRIPT ENDS
>
> I would like to make the dots representing the snps larger. I tried e.g.
>
> dp = DisplayPars(cex = 2) and dp = DisplayPars(size = 2) in the snpPlot definition without success and I can't work out the answer from the documentation.
>
> Incidentally I'm aware that the above script is perhaps abusing makeGenericArray - it works for me. If anyone has a more 'proper' way of doing this then that would be educational as well.
>
> Best
>
> Iain
>


-- 
Joern Toedling, PhD
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de
Tel.: +49 6131 39 21511