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Old 11-26-2014, 04:14 AM   #1
Neytiri
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Location: London

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Default 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!
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Old 12-02-2014, 01:35 AM   #2
areyes
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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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Old 12-02-2014, 03:32 AM   #3
Neytiri
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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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Old 12-02-2014, 04:27 AM   #4
areyes
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Quote:
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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