R help - Feb 2010 - 3D plot

Dearl list,

can anyone point me to a function or library that can create a graph similar to
the one in the following powerpoint presentation?

http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt

(pages 36-37)

In order to try to explain the graph, the way I see it in R terms is something
like this:

the "p-q" axis is a vector of positions (for example,
seq(0,5000000,1))
the "Chr1-Chrx" is a vector of units, in this case chromosomes (so
something like seq(1,10,1))
the plotted data is observations for each unit at each position

I guess the fancy gradient on the highest peaks is tougher to get (knowing I am
not an R expert), but just plain blue would suffice.

I have checked some of the graphs in the R graph gallery but I don´t think any
of them would work

Thanks in advance,

Dave
 		 	   		  
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On 02/19/2010 03:43 AM, David A.G wrote:
>
> Dearl list,
>
> can anyone point me to a function or library that can create a graph
similar to the one in the following powerpoint presentation?
>
> http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt
>
> (pages 36-37)
>
> In order to try to explain the graph, the way I see it in R terms is
something like this:
>
> the "p-q" axis is a vector of positions (for example,
seq(0,5000000,1))
> the "Chr1-Chrx" is a vector of units, in this case chromosomes
(so something like seq(1,10,1))
> the plotted data is observations for each unit at each position
>
> I guess the fancy gradient on the highest peaks is tougher to get (knowing
I am not an R expert), but just plain blue would suffice.
>
> I have checked some of the graphs in the R graph gallery but I don?t think
any of them would work
>
Hi Dave,
This is a sort of 2.5D plot, with each chromosome being a 2D plot spaced 
out on the z axis. If we assume that it is a static viewpoint, it would 
be a case of drawing the parallelogram "base", then overlaying a 
sequence of polygons with the appropriate offset to give the 3D 
appearance. My eyeball says that there is no perspective correction.

Doable, but I would advise asking on the Bioconductor mailing list first.

Jim

On 18/02/2010 11:43 AM, David A.G wrote:
> Dearl list,
> 
> can anyone point me to a function or library that can create a graph
similar to the one in the following powerpoint presentation?
It could be done in rgl with a lot of work.  I don't know of a package 
where someone has already done the work.

rgl can plot triangles and quadrilaterals in 3d, but not general 
polygons.  So you'd need to decompose each chromosome sequence into a 
sequence of simpler shapes.  For example,

n <- 100
f <- rnorm(n, mean=10, sd=1)
g <- rnorm(n, mean=10, sd=1)
x <- 1:n
fn <- colorRamp(c("blue","white","red"))
color <- function(value) {
   vals <- fn(value)
   rgb(vals[,1], vals[,2], vals[,3], max=255)
}

m <- max(f,g)

quadx <- cbind( x[-n], x[-1], x[-1], x[-n] )
quadh <- cbind( 0, 0, f[-1], f[-n] )
quadcol <- cbind( color(0), color(0), color(f[-1]/m), color(f[-n]/m))


quads3d( as.numeric(t(quadx)), 10, as.numeric(t(quadh)), 
col=as.character(t(quadcol)))
quadh <- cbind( 0, 0, g[-1], g[-n] )
quadcol <- cbind( color(0), color(0), color(g[-1]/m), color(g[-n]/m))
quads3d( as.numeric(t(quadx)), 20, as.numeric(t(quadh)), 
col=as.character(t(quadcol)))

This doesn't get the colours the way the presentation had them, that 
would be a bit more work.

Duncan Murdoch
> 
> http://bmi.osu.edu/~khuang/IBGP705/BMI705-Lecture7.ppt
> 
> (pages 36-37)
> 
> In order to try to explain the graph, the way I see it in R terms is
something like this:
> 
> the "p-q" axis is a vector of positions (for example,
seq(0,5000000,1))
> the "Chr1-Chrx" is a vector of units, in this case chromosomes
(so something like seq(1,10,1))
> the plotted data is observations for each unit at each position
> 
> I guess the fancy gradient on the highest peaks is tougher to get (knowing
I am not an R expert), but just plain blue would suffice.
> 
> I have checked some of the graphs in the R graph gallery but I don?t think
any of them would work
> 
> Thanks in advance,
> 
> Dave
>  		 	   		  
> _________________________________________________________________
> Hotmail: Trusted email with powerful SPAM protection.
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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