Dear all,
I have a collection of 5000 entries which represent the evolutionary
rates of 3 animals.
I would like to show the differences between the rates of all 3
animals and have tried using the function parallel (from the lattice
package) and pairs() function.
The parallel function would have been perfect save for the large
number of data (5000). The pairs() function doesn't show the
difference explicitly. Does anyone have any suggestions on
representing such data or have done similar plots?
I attach some simulated data:
mat3 <-matrix(sample(1:5000),nrow=5000,ncol=3, byrow=TRUE)
colnames(mat3) <- c("human","mouse", "chicken")
mat3 <-data.frame(mat3)
mat2$model <- factor( rep( "Model 3"), labels="model3")
## code I used for parallel
require(lattice)
parallel( ~ mat3[1:3]|model , mat3,varnames = c("human\ndnds",
"mouse
\ndnds", "chicken\ndnds") )
any suggestions or pointers would be greatly appreciated.
many thanks
tania
D.phil student
Department of Physiology, Anatomy and Genetics
sorry, I made a slight typo in the code below, it should be
mat3 <-matrix(sample(1:5000),nrow=5000,ncol=3, byrow=TRUE)
colnames(mat3) <- c("human","mouse", "chicken")
mat3 <-data.frame(mat3)
mat3$model <- factor( rep( "Model 3"), labels="model3")
## code I used for parallel
require(lattice)
parallel( ~ mat3[1:3]|model , mat3,varnames = c("human\ndnds",
"mouse
\ndnds", "chicken\ndnds") )
so very sorry to clog up your inboxes,
tania
On 3 Oct 2008, at 15:17, Tania Oh wrote:
> Dear all,
>
> I have a collection of 5000 entries which represent the evolutionary
> rates of 3 animals.
>
> I would like to show the differences between the rates of all 3
> animals and have tried using the function parallel (from the lattice
> package) and pairs() function.
>
> The parallel function would have been perfect save for the large
> number of data (5000). The pairs() function doesn't show the
> difference explicitly. Does anyone have any suggestions on
> representing such data or have done similar plots?
>
> I attach some simulated data:
>
> mat3 <-matrix(sample(1:5000),nrow=5000,ncol=3, byrow=TRUE)
> colnames(mat3) <- c("human","mouse",
"chicken")
> mat3 <-data.frame(mat3)
> mat2$model <- factor( rep( "Model 3"),
labels="model3")
>
>
> ## code I used for parallel
>
> require(lattice)
> parallel( ~ mat3[1:3]|model , mat3,varnames = c("human\ndnds",
"mouse
> \ndnds", "chicken\ndnds") )
>
>
> any suggestions or pointers would be greatly appreciated.
>
> many thanks
> tania
>
> D.phil student
> Department of Physiology, Anatomy and Genetics
>
>
>
Typical suggestions would be to sample from the data or use alpha blending (translucency). Best wishes; uwe Ligges Tania Oh wrote:> Dear all, > > I have a collection of 5000 entries which represent the evolutionary > rates of 3 animals. > > I would like to show the differences between the rates of all 3 animals > and have tried using the function parallel (from the lattice package) > and pairs() function. > > The parallel function would have been perfect save for the large number > of data (5000). The pairs() function doesn't show the difference > explicitly. Does anyone have any suggestions on representing such data > or have done similar plots? > > I attach some simulated data: > > mat3 <-matrix(sample(1:5000),nrow=5000,ncol=3, byrow=TRUE) > colnames(mat3) <- c("human","mouse", "chicken") > mat3 <-data.frame(mat3) > mat2$model <- factor( rep( "Model 3"), labels="model3") > > > ## code I used for parallel > > require(lattice) > parallel( ~ mat3[1:3]|model , mat3,varnames = c("human\ndnds", > "mouse\ndnds", "chicken\ndnds") ) > > > any suggestions or pointers would be greatly appreciated. > > many thanks > tania > > D.phil student > Department of Physiology, Anatomy and Genetics > > ______________________________________________ > R-help at 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.