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
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