Date: 2012-02-20 21:45 Sender: Benedikt HaugAdditional info:
By coloring the subset in a way like this...
add.plot(snp.subset(gwas.FT.ibs, snpsubset=unionframes), col=rep(colors()[c(552,255,456)]))
... the subset seems to get colored chromosomewise. By that I understood that the combination of add.plot(snp.subset(data,snpsupset)) does not take into account the snp positions of the previous (in my case full genome) plot(data) but just 'pastes' the subset together where chromosomes end (instead of inserting an appropriate spacer here). This is clearly visible as the first SNP of Chr2 (of the subset) is plotted upon the last snp of Chr1 (of the subset), the first of Chr3(...) upon the last of Chr 2(...) and so forth, leading to an increasing misalignment with the existing Manhattanplot with increasing chromosome number.
This is surprising, since as I wrote, on Chromosome one SNPs perfectly align, so that here a correct spacer seems to get inserted at the beginning (left of the first snp of the subset).
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