On Tue, Aug 4, 2009 at 12:58 AM, Patrick Aboyoun <paboyoun@fhcrc.org> wrote:

> Purna,
> Are you looking to visualize the letters or the locations? If its the
> locations your after, you might want to look to see what rtracklayer (genome
> browser integration), GenomeGraphs (plots genomic information from Ensembl)
> and HilbertVis (maps 1d vector into 2d space for better understanding of
> spatial relationships) have to offer. Their respective vignettes are at
>
>
> http://bioconductor.org/packages/2.5/bioc/vignettes/rtracklayer/inst/doc/rtracklayer.pdf


For rtracklayer, the simplest way is:

browseGenome(GenomicData(mychr, genome = "hg18"))

That assumes your reference genome is hg18.


>
> http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf
>
> http://bioconductor.org/packages/2.5/bioc/vignettes/HilbertVis/inst/doc/HilbertVis.pdf
>
> You may need help getting your data into a form to feed into a graph that
> interests you. If so, make sure you provide specifics like your R
> sessionInfo(), the reference genome you are using, and any other information
> that can help others help you.
>
>
> Patrick
>
>
>
> Purnachander wrote:
>
>> Dear all,
>>
>> I've loaded a complete genome into variable "mychr" and created many views
>> of it.
>> How can I represent all the generated views in a graphical plot?
>>
>> " mychr" is :
>>  1860725-letter "DNAString" instance
>> seq:
>> TGGTACCGGAAGCTATGCGTTAAAAAAGGAATAATG...GCAATTACCGGTAACGAAAAATTTCATGCGCCTTTC
>>
>> Views generated are :
>> views:
>>       start     end width
>>  [1]    2231   11434  9204
>> [GAGGTATGGAAACCTGATCTAGCC...TTCACCATAGTCGATTATAACAC]
>>  [2]   11784   18426  6643
>> [GTCACATCCGGGATTTTGCTCTGG...CCTTTTCTTCGTTGAGAAATTTC]
>>   ...     ...     ...   ... ...
>> [366] 1851121 1856489  5369
>> [GAAGTGGTAACCTCTGATCCTTCA...CATCATCATGAAGTCGAACGGAT]
>> [367] 1858686 1860020  1335
>> [TTCAAATGTTCGTAATACTTTTCA...ACGAATCTTGCCAACCTCATAGT]
>>
>> How can I graphically represent these views on a reference genome?
>>
>> Regards,
>> Purna
>>
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>>
>
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