[Bioc-sig-seq] ploting paired-end reads using GenomeGraphs

Kasper Daniel Hansen khansen at stat.berkeley.edu
Thu Dec 17 15:24:19 CET 2009


library(GenomeGraphs)
test <- new("MappedRead", start = 1:10, end = 4:13, strand = rep(c("+", "-"), each = 5))
gdPlot(test, minBase = 1, maxBase = 13)

There is no analogue to makeBaseTrack for example.  You'll notice that the reads are colored according to strand.

All that needs to be done is essentially to have start1, start2, end1, end2 and then draw small rectangle, line, small rectangle, for each read.

Kasper


On Dec 17, 2009, at 9:14 AM, Ramzi TEMANNI wrote:

> Hi Kasper,
> Thanks for your reply,
> I've take a look at the Reference Manual but unfortunately there's no example on how MappedReads class works.
> If you are familiar with it, could you please send me a quick example on how it works ?
> Thanks in advance,
> Regards,
> Ramzi
> ----------------------------------------------------------------
> 
> 
> On Thu, Dec 17, 2009 at 2:37 PM, Kasper Daniel Hansen <khansen at stat.berkeley.edu> wrote:
> There is a MappedRead class, but I think right now it only supports single-end.  It would however be more or less trivial to extend to paired end reads.  I have cc'ed the GenomeGraphs people.
> 
> Kasper
> 
> On Dec 17, 2009, at 8:24 AM, Ramzi TEMANNI wrote:
> 
> > Hi,
> > I would be interested in plotting the paired reads in a specific area of the
> > genome to have a nice representation of the distribution of paired reads .
> > Suppose we would like to visualize reads in this area:
> > chr7:13730853-14031050
> > i found out that the GenomeGraphs package can provide different
> > possibilities for plotting such data
> > using the following code :
> > library(GenomeGraphs)
> > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > ideogram <- makeIdeogram(chromosome = 7)
> > genomeAxis <- makeGenomeAxis(add53 = TRUE,
> >    add35 = TRUE)
> > gdPlot(list(ideogram, genomeAxis), minBase = 13730853, maxBase = 14031050)
> > I get a template with the idiogram and an axis of the area of intrest.
> >
> > How can I add the paired reads to that template (drowing rectangles
> > [pos.m1--pos.m2])?
> >
> >       CHR.M1   POS.M1 DIR.M1 CHR.M2    POS.M2 DIR.M2       GAP
> > 452475   chr7 13733464      -   chr7  13736747      +      3283
> > 310647   chr7 13739099      -   chr7  13742564      +      3465
> > 642995   chr7 13740159      -   chr7  13743227      +      3068
> > 124021   chr7 13743838      -   chr7  13747629      +      3791
> > 145136   chr7 13747724      -   chr7  13751470      +      3746
> > 95433    chr7 13752663      -   chr7  13756523      +      3860
> > 349071   chr7 13754592      -   chr7  13758004      +      3412
> > 578333   chr7 13764031      -   chr7  13767173      +      3142
> > 729375   chr7 13793339      -   chr7  13796280      +      2941
> > 39128    chr7 13862817      -   chr7  13866904      +      4087
> > 621938   chr7 13867663      -   chr7  13870756      +      3093
> > 841914   chr7 13870339      +   chr7  13870692      -       353
> > 204578   chr7 13873601      -   chr7  13877234      +      3633
> > 414932   chr7 13877564      -   chr7  13880892      +      3328
> > 450397   chr7 13878852      -   chr7  13882138      +      3286
> > 594118   chr7 13880502      -   chr7  13883627      +      3125
> > 276694   chr7 13884763      -   chr7  13888278      +      3515
> > 389308   chr7 13887051      -   chr7  13890410      +      3359
> > 42539    chr7 13895684      -   chr7  13899746      +      4062
> > 117314   chr7 13896500      -   chr7  13900307      +      3807
> > 251549   chr7 13901220      -   chr7  13904774      +      3554
> > 608668   chr7 13915635      -   chr7  13918743      +      3108
> > 847653   chr7 13920433      +   chr7  13920728      -       295
> > 67139    chr7 13933413      -   chr7  13937358      +      3945
> > 182569   chr7 13937777      -   chr7  13941450      +      3673
> > 294702   chr7 13938511      -   chr7  13941999      +      3488
> > 535133   chr7 13942971      -   chr7  13946161      +      3190
> > 515881   chr7 13943523      -   chr7  13946735      +      3212
> > 698816   chr7 13951296      -   chr7  13954289      +      2993
> > 741044   chr7 13953294      -   chr7  13956211      +      2917
> > 237927   chr7 13959649      -   chr7  13963225      +      3576
> > 124263   chr7 13961471      -   chr7  13965262      +      3791
> > 806523   chr7 13971198      -   chr7  13973008      +      1810
> > 342437   chr7 13982437      -   chr7  13985858      +      3421
> > 374119   chr7 13985689      -   chr7  13989068      +      3379
> >
> > Thanks in advance for your suggestion.
> >
> > Kind regards,
> > Ramzi
> > ----------------------------------------------------------------
> >
> >       [[alternative HTML version deleted]]
> >
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> 
> 



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