Entering edit mode
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????????
>
