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  • Gviz - adjust track height

    Dear all,

    I have a probably trivial problem where I need a hint into the right direction:

    I am trying to visualize RNA-seq data in Gviz (nice!). I have two bam files loaded as AlignmentsTrack (just coverage and sashimi, no reads). Individually, they fill the square plotting area completey (the Y-axis is scaled to fill all available space). I can also add GenomeAxisTrack and a BioMartGeneRegionTrack, which reduces the height accordingly. But when I add the second AlignmentsTrack, the plot no longer scales in y-direction and I get a very narrow band in the middle of my square plotting area (maybe 25% of the available space).

    How can I scale the two AlignmentsTracks to use more y-space in the plotting area? The parameters "sizes" or any type of "height" parameter just affects the ratio within the band, but not the overall size.



    Code:
    gTrack<-GenomeAxisTrack()
    alTrack<-AlignmentsTrack(range='WT.bam',genome='hg19', name='Wildtype', chromosome='chr8',ispaired=T)
    alTrack2<-AlignmentsTrack(range='Mut.bam',genome='hg19', name='Mutant', chromosome='chr8',ispaired=T)
    bmt<-BiomartGeneRegionTrack(genome='hg19',chromosome='chr8',start=afrom,end=ato,filter=list(with_ox_refseq_mrna=T),stacking='squish',showExonId=F)
    plotTracks(c(gTrack,bmt,alTrack,alTrack2),from=afrom,to=ato,type=c('coverage','sashimi'))

  • #2
    Did you have the same problem as I'm experiencing here? If so, did you ever find a solution?

    Edit: If that was your problem, the solution is in the thread I linked to
    Last edited by stianlagstad; 04-20-2016, 01:07 PM.

    Comment


    • #3
      Hi,

      thanks for pointing me to your thread. Meanwhile, I have given up on this problem, but although my plot is slightly different, I'll give the max.height parameter a try.

      Markus

      Comment


      • #4
        If you provide a runnable code example (not dependent on your own data sets), it will be much easier to understand what the problem is See some tips for how to do that here: How to create a Minimal, Complete, and Verifiable example

        Comment


        • #5
          You could also use the gapped.bam from the Gviz sample data twice:
          bamFile<-system.file("extdata/gapped.bam",package="Gviz")
          gTrack<-GenomeAxisTrack()
          alTrack<-AlignmentsTrack(range=bamFile,genome='hg19', name='Wildtype', chromosome='chr12',ispaired=T)
          alTrack2<-AlignmentsTrack(range=bamFile,genome='hg19', name='Mutant', chromosome='chr12',ispaired=T)
          plotTracks(c(gTrack,alTrack,alTrack2),from=2965000,to=3000000,type=c('coverage','sashimi'))
          Setting the min.height parameter did not change it, unfortunately.

          Comment


          • #6
            Executable code - great! So this code:

            Code:
            bamFile <- system.file(
              "extdata/gapped.bam",
              package = "Gviz")
            gTrack <- GenomeAxisTrack()
            alTrack<- AlignmentsTrack(
              range = bamFile,
              genome = 'hg19',
              name = 'Wildtype',
              chromosome = 'chr12',
              ispaired = T)
            alTrack2 <- AlignmentsTrack(
              range = bamFile,
              genome = 'hg19',
              name = 'Mutant',
              chromosome = 'chr12',
              ispaired = T)
            plotTracks(
              c(gTrack, alTrack, alTrack2),
              from = 2965000,
              to = 3000000,
              type = c('coverage', 'sashimi'))
            Produces this plot for me:



            To me it looks like the available y-space is used. What exactly is the problem?

            Comment


            • #7
              I attached what it produces on my system. I saved it as pdf, though, because that format is easiest to use in Illustrator.
              Code:
              pdf('test.pdf')
              plotTracks(
                c(gTrack, alTrack, alTrack2),
                from = 2965000,
                to = 3000000,
                type = c('coverage', 'sashimi'))
              dev.off()
              EDIT: png gives the same
              Attached Files
              Last edited by abisko00; 04-21-2016, 01:16 AM. Reason: more info

              Comment


              • #8
                I see. I'm also experiencing these issues when exporting Gviz plots to pdf. Maybe you could try using svg instead? I don't know whether this is a problem with Gviz or with the pdf device, but you could ask a question over at the Bioconductor support site. The Gviz author, Florian Hahne, is responsive to questions there.

                Comment


                • #9
                  How did you produce your image? I am relatively new to R and completely autodidactic. Maybe I miss a very simple setting. But thanks anyway!

                  Comment


                  • #10
                    If you mean the plot in my post above, I exported it as a png image from RStudio. But you could also do this:

                    Code:
                    png(
                      'test.png',
                      width = 600,
                      height = 300)
                    plotTracks(
                      c(gTrack, alTrack, alTrack2),
                      from = 2965000,
                      to = 3000000,
                      type = c('coverage', 'sashimi'))
                    dev.off()
                    Or you could switch png with svg, pdf or something else. A list of available plotting devices can be found here.

                    Comment


                    • #11
                      Solved

                      Normally, I hate these kind of solutions, because you learn nothing from them, but after you've shown that the code is working, I did a clean install of R and Gviz and here we go!

                      Thanks!
                      Attached Files

                      Comment

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