GenomeGraphs question
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@iain-gallagher-2532
Last seen 9.3 years ago
United Kingdom
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 > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: ?[1] LC_CTYPE=en_GB.utf8?????? LC_NUMERIC=C???????????? ?[3] LC_TIME=en_GB.utf8??????? LC_COLLATE=en_GB.utf8??? ?[5] LC_MONETARY=en_GB.utf8??? LC_MESSAGES=en_GB.utf8?? ?[7] LC_PAPER=C??????????????? LC_NAME=C??????????????? ?[9] LC_ADDRESS=C????????????? LC_TELEPHONE=C?????????? [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C????? attached base packages: [1] grid????? stats???? graphics? grDevices utils???? datasets? methods? [8] base???? other attached packages: [1] GenomeGraphs_1.14.0 biomaRt_2.10.0????? ggplot2_0.9.0????? loaded via a namespace (and not attached): ?[1] colorspace_1.1-1?? dichromat_1.2-4??? digest_0.5.1?????? MASS_7.3-16?????? ?[5] memoise_0.1??????? munsell_0.3??????? plyr_1.7.1???????? proto_0.3-9.2???? ?[9] RColorBrewer_1.0-5 RCurl_1.9-5??????? reshape2_1.2.1???? scales_0.1.0????? [13] stringr_0.6??????? tools_2.14.1?????? XML_3.9-2???????? >
SNP biomaRt ideogram GenomeGraphs SNP biomaRt ideogram GenomeGraphs • 1.5k views
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@joern-toedling-4741
Last seen 10.2 years ago
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
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