[Bioc-sig-seq] How to graphical represent different views on a reference genomic sequence

[Patrick Aboyoun]

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
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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