richard mendes wrote:
> Hello Sean,
> The code that i was using was simply pasting the same code in python.
> r("i<-1") # i should use the attach statement i think
> r("while (i <= length(groups) ) {")
> r("png(file=sprintf('MAplot%03d.png', i), width=600, height=600)")
> r("MAplot(rawAffyData, pairs=TRUE, plot.method='smoothScatter'
> which=groups[[i]])")
> r("dev.off()")
> r("i<-i+1 }")
>
> But i expect that using rpy in such a way is completely wrong. I'm just
> testing what can be done by rpy
Options:
* Try sticking all your string commands in one long string and running
it all at once.
>>> loop="i=0;while(i<10){i=i+1}"
>>> r(loop)
10.0
* Write your loop in Python, and only call png and MAplot using Rpy.
You'll learn how to pass variables between python and R too!
>>> for i in range(len(r.groups)):
... print i
will loop from 0 to length(groups)-1 (python starts indexes at 0)
Then do:
>>> r.assign("i",i+1)
- this creates an R object with the value of the python 'i' + 1
Then do your calls inside the loop. No need to increment the 'i' in R,
your loop controller is now a python variable. You should end up with
this (untested):
for i in range(len(r.groups)):
r.assign("i",i+1)
r("png(file=sprintf('MAplot%03d.png', i), width=600, height=600)")
r("MAplot(rawAffyData, pairs=TRUE, plot.method='smoothScatter'
which=groups[[i]])")
r("dev.off()")
> Currently they have rserve running on a server that connects several app's
> to R. The only problem is that i couldn't
> find a interface between python and rserve.
I half-wrote this and then discovered Rpy. I have an alpha version if
you want it, but trust me, you probably don't want it. It was at the
'now this is a real mess, it needs rewriting from scratch' stage.
Barry
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