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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