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  • Ideas for graphing data?

    I have developed a method that identifies some genomic features and does so tissue-specifically. Now I would like to make some visual representation of this. E.g in one type of tissue I get lets say 1000 hits of varying intensity across the genome chromosomes. In other tissues I could get lets say 500-1500 hits of varying intensity across chromosomes.

    It can be boiled down to a genomic coordinate accompanied by a intensity/frequency score. The coordinate is not super-important for the graphical representation, hence no need to depict the exact chromosome, however it would aid interpretation I guess.

    Is there some 'fancy' way of doing this besides a heatmap or the like for every chromosome?

    All inputs appreciated.

  • #2
    Circos plots?

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    • #3
      Originally posted by blancha View Post
      Circos plots?
      I second this. Circos plot with histogram tracks for each tissue could look really good. The only problem I can see would be resolution. If you want to show differences within small ranges (eg. Differences in histone marks within a 100kb range), this may not be best. Because the plot represents the whole genome, a single pixel often represents ~1Mb. However if you can bin your values into ~1Mb windows, you're golden.

      aesthetics,alignment,analysis,bioinformatics,cancer,circos,circular,comparative,conservation,data visualization,design,evolution,evolutionary,gene,genetic,genome,genome sciences centre,genomic,genomics,graph,graphics,human,human genome,infovis,martin krzywinski,rearrangement,science,sequence,somatic,structural,synteny

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      • #4
        Some guy named Ying Hu wrote some Circos thing in R (Who?)



        OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

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