generic question -> Genomics with R

classic Classic list List threaded Threaded
14 messages Options
Reply | Threaded
Open this post in threaded view
|

generic question -> Genomics with R

Ricardo Rodríguez
Hi everybody,

I am trying to make my mind about the use of R for Computational and
Statistical Approaches to Genomics.

I know this is a vaste field: this is the main reason why I am sending
this message to this always useful list! Any key/entry point to this
field will be extremely welcome!

Please, could you help me to go in the right direction?

Thanks!!!

Ricardo

--
Ricardo Rodríguez
Your XEN ICT Team

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: generic question -> Genomics with R

Liviu Andronic
Hello,

On 4/29/08, [Ricardo Rodriguez] Your XEN ICT Team <[hidden email]> wrote:
>  I am trying to make my mind about the use of R for Computational and
> Statistical Approaches to Genomics.
>
[..]
>  Please, could you help me to go in the right direction?
>
I am not sure what pointers you are looking for, but checking the CRAN
Task Views [1] may be a starting point.

Liviu
[1] http://cran.r-project.org/web/views/index.html

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: generic question -> Genomics with R

Richard Pearson-2
I'd also suggest you check out http://www.bioconductor.org - "Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data"

Richard.

Liviu Andronic wrote:

> Hello,
>
> On 4/29/08, [Ricardo Rodriguez] Your XEN ICT Team <[hidden email]> wrote:
>>  I am trying to make my mind about the use of R for Computational and
>> Statistical Approaches to Genomics.
>>
> [..]
>>  Please, could you help me to go in the right direction?
>>
> I am not sure what pointers you are looking for, but checking the CRAN
> Task Views [1] may be a starting point.
>
> Liviu
> [1] http://cran.r-project.org/web/views/index.html
>
> ______________________________________________
> [hidden email] mailing list
> 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.
>

--
Richard D. Pearson             [hidden email]
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
University of Manchester,      Tel: +44 161 275 6178
Oxford Road,                   Mob: +44 7971 221181
Manchester M13 9PL, UK.        Fax: +44 161 275 6204

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: generic question -> Genomics with R

Bart Joosen
In reply to this post by Ricardo Rodríguez
I'm not sure what you are trying to do with R, but maybe you should take a look at the Task Views and see if there is something you can use at your field of work:
http://www.stats.bris.ac.uk/R/web/views/


Bart


Ricardo Rodríguez wrote
Hi everybody,

I am trying to make my mind about the use of R for Computational and
Statistical Approaches to Genomics.

I know this is a vaste field: this is the main reason why I am sending
this message to this always useful list! Any key/entry point to this
field will be extremely welcome!

Please, could you help me to go in the right direction?

Thanks!!!

Ricardo

--
Ricardo Rodríguez
Your XEN ICT Team

______________________________________________
R-help@r-project.org mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: generic question -> Genomics with R

Ricardo Rodríguez
Thank you so much. All the answers lead me to BioConductor and Task
Views. Currently, I've not a precise task to solve, but I do need to
draw a landscape about this topic. Your messages have helped a lot.

I don't know why, but I don't reach BioConductor website by googling or
searchmashing.

Cheers,

Ricardo.


bartjoosen wrote:
> I'm not sure what you are trying to do with R, but maybe you should take a
> look at the Task Views and see if there is something you can use at your
> field of work:
> http://www.stats.bris.ac.uk/R/web/views/
>
>
> Bart


--
Ricardo Rodríguez
Your XEN ICT Team

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

How to plot wind direction and strength field

Jenny Barnes
Dear R-help community,

I have searched through the archives and not been able ot find any advice
on how to plot a wind field with one arrow per grid square with the arrow
pointing in the direction of the wind and it's size proportional to the
wind strength.

I have the wind speed data in arrays of [lon,lat,uwind] and
[lon,lat,vwind] so it is broken down into u and v components. How do I
plot it though?!?!

Any suggestions very wecome indeed - I seem to have hit a brick wall.....

All the best,

Jenny

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jennifer Barnes
PhD student: long range drought prediction
Climate Extremes Group
Department of Space and Climate Physics
University College London
Holmbury St Mary
Dorking, Surrey, RH5 6NT
Web: http://climate.mssl.ucl.ac.uk

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Jim Lemon
Jenny Barnes wrote:

> Dear R-help community,
>
> I have searched through the archives and not been able ot find any
> advice on how to plot a wind field with one arrow per grid square with
> the arrow pointing in the direction of the wind and it's size
> proportional to the wind strength.
>
> I have the wind speed data in arrays of [lon,lat,uwind] and
> [lon,lat,vwind] so it is broken down into u and v components. How do I
> plot it though?!?!
>
> Any suggestions very wecome indeed - I seem to have hit a brick wall.....

Hi Jenny,
Some time ago, there was a request for a direction field plot. I
programmed a basic function, but perhaps the person found another
solution, for I never heard any more of it. However, this is not too
hard to do in R, even adding the arrows to a geographical plot. Could
you post some data and perhaps a link to an example of what output you
would like?

Jim

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Jenny Barnes
Hi Jim,

I would like to plot something like figure 2 on this webpage:
http://www.cnrfc.noaa.gov/storm_summaries/jan1997storms.php

My data is very large - covering the whole globe at 2.5deg resolution so
longitude=144 girds, latitude=73 grids and time=32 years - hard to give
you that data......Would it help to give you a couple of grid squares
worth of data for one year?

Thanks,

Jenny

On Tue, 29 Apr 2008, Jim Lemon wrote:

> Jenny Barnes wrote:
>> Dear R-help community,
>>
>> I have searched through the archives and not been able ot find any advice
>> on how to plot a wind field with one arrow per grid square with the arrow
>> pointing in the direction of the wind and it's size proportional to the
>> wind strength.
>>
>> I have the wind speed data in arrays of [lon,lat,uwind] and [lon,lat,vwind]
>> so it is broken down into u and v components. How do I plot it though?!?!
>>
>> Any suggestions very wecome indeed - I seem to have hit a brick wall.....
>
> Hi Jenny,
> Some time ago, there was a request for a direction field plot. I programmed a
> basic function, but perhaps the person found another solution, for I never
> heard any more of it. However, this is not too hard to do in R, even adding
> the arrows to a geographical plot. Could you post some data and perhaps a
> link to an example of what output you would like?
>
> Jim
>
>

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Sean O'Riordain
In reply to this post by Jenny Barnes
Jenny,

Have a look at the R Newsletter Volume 3/2, October 2003

Regards,
Sean

Jenny Barnes wrote
Dear R-help community,

I have searched through the archives and not been able ot find any advice
on how to plot a wind field with one arrow per grid square with the arrow
pointing in the direction of the wind and it's size proportional to the
wind strength.

I have the wind speed data in arrays of [lon,lat,uwind] and
[lon,lat,vwind] so it is broken down into u and v components. How do I
plot it though?!?!

Any suggestions very wecome indeed - I seem to have hit a brick wall.....

All the best,

Jenny

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jennifer Barnes
PhD student: long range drought prediction
Climate Extremes Group
Department of Space and Climate Physics
University College London
Holmbury St Mary
Dorking, Surrey, RH5 6NT
Web: http://climate.mssl.ucl.ac.uk

______________________________________________
R-help@r-project.org mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Gabor Grothendieck
In reply to this post by Jenny Barnes
Check out:

http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=80

and

RSiteSearch("quiver")


On Tue, Apr 29, 2008 at 6:08 AM, Jenny Barnes <[hidden email]> wrote:

> Dear R-help community,
>
> I have searched through the archives and not been able ot find any advice on
> how to plot a wind field with one arrow per grid square with the arrow
> pointing in the direction of the wind and it's size proportional to the wind
> strength.
>
> I have the wind speed data in arrays of [lon,lat,uwind] and [lon,lat,vwind]
> so it is broken down into u and v components. How do I plot it though?!?!
>
> Any suggestions very wecome indeed - I seem to have hit a brick wall.....
>
> All the best,
>
> Jenny
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Jennifer Barnes
> PhD student: long range drought prediction Climate Extremes Group
> Department of Space and Climate Physics
> University College London
> Holmbury St Mary Dorking, Surrey, RH5 6NT
> Web: http://climate.mssl.ucl.ac.uk
>
> ______________________________________________
> [hidden email] mailing list
> 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.
>

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Jenny Barnes
In reply to this post by Jenny Barnes
Thanks Jim - here is some data:

u <- array(NA,c(5,8))
t <- seq(from=0.5, to=0.11,length=15)
t2 <- seq(from=(-0.7),to=(-0.1),length=25)
u[1:15] <- t
u[16:40] <- t2
v <- array(NA,c(5,8))
y <- seq(from=(-0.9), to=(-0.01),length=40)
v[1:40] <- y

I've made up the data but it's similar magnitude and the longitude
direction is u and latitude direction is v as in the real data.

I really appreciate your help!

Jenny

On Tue, 29 Apr 2008, Jim Lemon wrote:

> Jenny Barnes wrote:
>> Hi Jim,
>>
>> I would like to plot something like figure 2 on this webpage:
>> http://www.cnrfc.noaa.gov/storm_summaries/jan1997storms.php
>>
>> My data is very large - covering the whole globe at 2.5deg resolution so
>> longitude=144 girds, latitude=73 grids and time=32 years - hard to give you
>> that data......Would it help to give you a couple of grid squares worth of
>> data for one year?
>>
> Okay, Figures 2 and 3 look like 5 degree squares, and given a larger plot,
> 2.5 degree should be okay. Do you want curved arrows? That would take some
> programming as the standard arrows are straight. Also, the arrows in the
> figures all seem to be the same length. I can make the lengths proportional
> to wind speed. Yes, some data would be helpful, as getting the right plot
> usually involves trying out real data. Doesn't matter if it's faked as long
> as it has the same format and similar numbers to the real thing.
>
> Jim
>
>
>

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Jenny Barnes
In reply to this post by Jenny Barnes
Hi Jim,

I forgot to say that I don't want to create curved arrows, just straight -
and I would like them to be proportional to the magnitude :o)

Thanks again for your time!

Jenny

On Tue, 29 Apr 2008, Jenny Barnes wrote:

> Hi Jim,
>
> I would like to plot something like figure 2 on this webpage:
> http://www.cnrfc.noaa.gov/storm_summaries/jan1997storms.php
>
> My data is very large - covering the whole globe at 2.5deg resolution so
> longitude=144 girds, latitude=73 grids and time=32 years - hard to give you
> that data......Would it help to give you a couple of grid squares worth of
> data for one year?
>
> Thanks,
>
> Jenny
>
> On Tue, 29 Apr 2008, Jim Lemon wrote:
>
>> Jenny Barnes wrote:
>>> Dear R-help community,
>>>
>>> I have searched through the archives and not been able ot find any advice
>>> on how to plot a wind field with one arrow per grid square with the arrow
>>> pointing in the direction of the wind and it's size proportional to the
>>> wind strength.
>>>
>>> I have the wind speed data in arrays of [lon,lat,uwind] and
>>> [lon,lat,vwind] so it is broken down into u and v components. How do I
>>> plot it though?!?!
>>>
>>> Any suggestions very wecome indeed - I seem to have hit a brick wall.....
>>
>> Hi Jenny,
>> Some time ago, there was a request for a direction field plot. I programmed
>> a basic function, but perhaps the person found another solution, for I
>> never heard any more of it. However, this is not too hard to do in R, even
>> adding the arrows to a geographical plot. Could you post some data and
>> perhaps a link to an example of what output you would like?
>>
>> Jim
>>
>>
>

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Greg Snow-2
In reply to this post by Jenny Barnes
Does the following do what you want (or at least move in that
direction)?

u <- array(NA,c(5,8))
t <- seq(from=0.5, to=0.11,length=15)
t2 <- seq(from=(-0.7),to=(-0.1),length=25)
u[1:15] <- t
u[16:40] <- t2
v <- array(NA,c(5,8))
y <- seq(from=(-0.9), to=(-0.01),length=40)
v[1:40] <- y

library(TeachingDemos)

library(maps)
map('state',col='grey')

lats <- seq( 27.5, 48.7, length=5 )
longs <- seq( -123, -73, length=8 )

x <- longs[ col(u) ]
y <- lats[ row(u) ]

speed <- sqrt( u*u+v*v )
dir <- atan2(v,u)

my.symbols(x,y,ms.arrows, angle=dir, r=speed, add=TRUE, length=.05)


Hope this helps,


--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[hidden email]
(801) 408-8111
 
 

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Jenny Barnes
> Sent: Tuesday, April 29, 2008 6:26 AM
> To: Jim Lemon
> Cc: [hidden email]
> Subject: Re: [R] How to plot wind direction and strength field
>
> Thanks Jim - here is some data:
>
> u <- array(NA,c(5,8))
> t <- seq(from=0.5, to=0.11,length=15)
> t2 <- seq(from=(-0.7),to=(-0.1),length=25)
> u[1:15] <- t
> u[16:40] <- t2
> v <- array(NA,c(5,8))
> y <- seq(from=(-0.9), to=(-0.01),length=40) v[1:40] <- y
>
> I've made up the data but it's similar magnitude and the
> longitude direction is u and latitude direction is v as in
> the real data.
>
> I really appreciate your help!
>
> Jenny
>
> On Tue, 29 Apr 2008, Jim Lemon wrote:
>
> > Jenny Barnes wrote:
> >> Hi Jim,
> >>
> >> I would like to plot something like figure 2 on this webpage:
> >> http://www.cnrfc.noaa.gov/storm_summaries/jan1997storms.php
> >>
> >> My data is very large - covering the whole globe at 2.5deg
> resolution
> >> so
> >> longitude=144 girds, latitude=73 grids and time=32 years - hard to
> >> give you that data......Would it help to give you a couple of grid
> >> squares worth of data for one year?
> >>
> > Okay, Figures 2 and 3 look like 5 degree squares, and given
> a larger
> > plot,
> > 2.5 degree should be okay. Do you want curved arrows? That
> would take
> > some programming as the standard arrows are straight. Also,
> the arrows
> > in the figures all seem to be the same length. I can make
> the lengths
> > proportional to wind speed. Yes, some data would be helpful, as
> > getting the right plot usually involves trying out real
> data. Doesn't
> > matter if it's faked as long as it has the same format and
> similar numbers to the real thing.
> >
> > Jim
> >
> >
> >
>
> ______________________________________________
> [hidden email] mailing list
> 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.
>

______________________________________________
[hidden email] mailing list
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.
Reply | Threaded
Open this post in threaded view
|

Re: How to plot wind direction and strength field

Jenny Barnes
Thanks Greg,

I'll give it a whirl and let you know how it goes (although it might not
be till after the bank holiday weekend now sorry for delay!)

Thanks for replying and spending time on this problem.

All the best,

Jenny

On Thu, 1 May 2008, Greg Snow wrote:

> Does the following do what you want (or at least move in that
> direction)?
>
> u <- array(NA,c(5,8))
> t <- seq(from=0.5, to=0.11,length=15)
> t2 <- seq(from=(-0.7),to=(-0.1),length=25)
> u[1:15] <- t
> u[16:40] <- t2
> v <- array(NA,c(5,8))
> y <- seq(from=(-0.9), to=(-0.01),length=40)
> v[1:40] <- y
>
> library(TeachingDemos)
>
> library(maps)
> map('state',col='grey')
>
> lats <- seq( 27.5, 48.7, length=5 )
> longs <- seq( -123, -73, length=8 )
>
> x <- longs[ col(u) ]
> y <- lats[ row(u) ]
>
> speed <- sqrt( u*u+v*v )
> dir <- atan2(v,u)
>
> my.symbols(x,y,ms.arrows, angle=dir, r=speed, add=TRUE, length=.05)
>
>
> Hope this helps,
>
>
> --
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> [hidden email]
> (801) 408-8111
>
>
>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Jenny Barnes
>> Sent: Tuesday, April 29, 2008 6:26 AM
>> To: Jim Lemon
>> Cc: [hidden email]
>> Subject: Re: [R] How to plot wind direction and strength field
>>
>> Thanks Jim - here is some data:
>>
>> u <- array(NA,c(5,8))
>> t <- seq(from=0.5, to=0.11,length=15)
>> t2 <- seq(from=(-0.7),to=(-0.1),length=25)
>> u[1:15] <- t
>> u[16:40] <- t2
>> v <- array(NA,c(5,8))
>> y <- seq(from=(-0.9), to=(-0.01),length=40) v[1:40] <- y
>>
>> I've made up the data but it's similar magnitude and the
>> longitude direction is u and latitude direction is v as in
>> the real data.
>>
>> I really appreciate your help!
>>
>> Jenny
>>
>> On Tue, 29 Apr 2008, Jim Lemon wrote:
>>
>>> Jenny Barnes wrote:
>>>> Hi Jim,
>>>>
>>>> I would like to plot something like figure 2 on this webpage:
>>>> http://www.cnrfc.noaa.gov/storm_summaries/jan1997storms.php
>>>>
>>>> My data is very large - covering the whole globe at 2.5deg
>> resolution
>>>> so
>>>> longitude=144 girds, latitude=73 grids and time=32 years - hard to
>>>> give you that data......Would it help to give you a couple of grid
>>>> squares worth of data for one year?
>>>>
>>> Okay, Figures 2 and 3 look like 5 degree squares, and given
>> a larger
>>> plot,
>>> 2.5 degree should be okay. Do you want curved arrows? That
>> would take
>>> some programming as the standard arrows are straight. Also,
>> the arrows
>>> in the figures all seem to be the same length. I can make
>> the lengths
>>> proportional to wind speed. Yes, some data would be helpful, as
>>> getting the right plot usually involves trying out real
>> data. Doesn't
>>> matter if it's faked as long as it has the same format and
>> similar numbers to the real thing.
>>>
>>> Jim
>>>
>>>
>>>
>>
>> ______________________________________________
>> [hidden email] mailing list
>> 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.
>>
>
>

______________________________________________
[hidden email] mailing list
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.