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 Similar Threads Thread Thread Starter Forum Replies Last Post velt Bioinformatics 1 03-05-2014 04:54 AM kushald Bioinformatics 1 05-15-2013 09:19 PM ziseputi Bioinformatics 3 03-07-2013 04:53 AM vplagnol RNA Sequencing 6 01-18-2013 04:45 AM seq_GA Bioinformatics 2 11-21-2011 01:34 PM

 11-26-2014, 04:14 AM #1 Neytiri Junior Member   Location: London Join Date: Nov 2012 Posts: 3 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!
 12-02-2014, 01:35 AM #2 areyes Senior Member   Location: Heidelberg Join Date: Aug 2010 Posts: 165 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
 12-02-2014, 03:32 AM #3 Neytiri Junior Member   Location: London Join Date: Nov 2012 Posts: 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!
12-02-2014, 04:27 AM   #4
areyes
Senior Member

Location: Heidelberg

Join Date: Aug 2010
Posts: 165

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

 Tags dexseq plot