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plotDEXSeq reorder x-axis

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  • plotDEXSeq reorder x-axis

    Hi,

    I'm using plotDEXSeq to visualize the results of a DEXSeq (v1.10.8) analysis: plotDEXSeq( dxr, gene).

    However, the exons listed in the x-axis show up by increasing order of padj, e.g. E025 E020 E010 E005 E006 E017 etc, being E025 the exon with the lowest padj. How can I re-order the x-axis so that the exons are listed in order, by their positions?

    Thank you!

  • #2
    Hi Neytiri,

    This sounds like a bug in the plotting function. Did you by chance modified the order of the results table? Could you send me a reproducible example to generate the plot that you mentioned as well as the output of your sessionInfo()?

    Alejandro

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    • #3
      Hi Alejandro,

      Thanks for your reply. After reading your post I understood the issue!

      When I do:
      > dxr = DEXSeqResults( dxd )
      > plotDEXSeq(dxr, gene)
      then the exons in the plot are ordered by their positions, i.e E001 E002 E003 etc.

      When I do:
      > dxr = DEXSeqResults( dxd )
      > dxr = dxr[order(dxr$padj),]
      > plotDEXSeq(dxr, gene)
      then the exons in the plot are ordered by increasing order of padj, e.g. E025 E020 E010 E005 E006 etc.

      My issue is now solved. Anyway, I think it would be nicer if reordering the object DEXSeqResults did not affect the order of the exons in the plot.

      Thanks again for your attention!

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      • #4
        My issue is now solved. Anyway, I think it would be nicer if reordering the object DEXSeqResults did not affect the order of the exons in the plot.
        I think I agree with you and I will fix this issue! Thanks for noticing it!

        Alejandro

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