My suggestion is to pay attention to Boris and ask people who do this kind
of plotting frequently... and they are typically found on the Bioconductor
mailing list, not this list.
On Sat, 28 Jul 2018, Bogdan Tanasa wrote:
Dear Boris,
good morning, and thank you for your message. After thinking a bit more
yesterday, I believe that I could adapt the functionality of some R
packages that display the synteny regions across multiple species (here
please see an example Figure 1 from http://www.g3journal.org/
content/7/6/1775.figures-only),
although I have not found yet a R package that does this display (in my
case, instead of distinct species, I will just show distinct chromosomes
connected by translocations). If you have any suggestions, please let me
know.
thanks a lot,
-- bogdan
On Sat, Jul 28, 2018 at 6:42 AM, Boris Steipe <boris.ste...@utoronto.ca>
wrote:
Maybe the Bioconductor package "intansv" can help you. You asked for
linear chromosomes, but such data is commonly plotted in Circos plots as
e.g. with the Bioconductor OmicsCircos package (cf.
https://bioconductor.org/packages/devel/bioc/vignettes/
OmicCircos/inst/doc/OmicCircos_vignette.pdf)
However the Bioconductor Project has its own support mailing list, R-Help
is for programming help.
B.
On 2018-07-28, at 02:24, Bogdan Tanasa <tan...@gmail.com> wrote:
Dear all,
we wish you a fruitful and refreshing weekend ! Thought that I may also
write to ask you for a suggestion, specifically if you could please
advise
on whether there is any package already built (in R) that could help with
the following data visualization :
we have a set of mutations from many cancer samples
we would like to display the POINT MUTATIONS along the chromosome
coordinates (on the linear scale, ie. HORIZONTALLY)
we would like to display the TRANSLOCATIONS (and GENE FUSIONS), as
VERTICAL LINES connecting the breakpoints that are located on the
chromosomes that are represented HORIZONTALLY
Thanks a lot,
-- bogdan
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/
posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
---------------------------------------------------------------------------
Jeff Newmiller The ..... ..... Go Live...
DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
