Open diegohernansanchez opened 8 months ago
Hi, Could you describe a bit more what you mean by Manhattan plot and what is your input data? Thanks, Lucille
Hi Lucille, Thanks for prompt response. Sure, a Manhattan plot depicts association-mapping data. This is a statistical correlation between a phenotype and detected genetic polymorphisms at population level. If a particular polymorphism (say a single nucleotide polymorphism -SNP-, which is a base variant in a particular chromosomal coordinate) occurs in a fraction of the population and is significantly correlated with a phenotype, then this polymorphism is given a lower p-value. Otherwise, non-correlated SNPs present a higher p-value. Hence, a Manhattan plot depicts -log(p-values) along chromosomal coordinates (see an example in https://en.wikipedia.org/wiki/Manhattan_plot). It would be very useful that pyGenomeTracks could handle this type of data over a genome browser, as genetic causality could be supported by comparison with additional genome-wide data such as RNA-seq, etc. The input data is simpler than a BED4, with just a single chromosomal coordinate instead of start-end. It would be a tab-delimited .txt file with columns: chromosome | position | -log(p-values). It is just needed to depict a dot in that position, with certain size and color, the latter usually depending on the chromosome number. Thanks for your time. Cheers diego
Hi,
type = points
or type = points:0.5
where you specify the point size. For example, if your input file has only 3 columns (chr | pos | -log(pval)) you can use awk
to convert it:
awk -v OFS="\t" '{print $1,$2,$2+1,$3}' input_3col.txt > output.bedgraph
.
Hi, Not really an Issue. I was wondering if you have at hand a solution to articulate Manhattan plot data on pyGenomeTracks Thanks diego