Importing delimited data

[Pizzalova]

Hi all,

I searched but I couldn't find a solution. When using R, I can import
a delimited file into an R data frame using read.table() function. I
uploaded the data using the notebook function, and I checked the
~/.sage/sage_notebook/../../data directory and the data appears to be
there. However, trying rpy through the notebook interface on Mac OSX I
get the following:

from rpy import *

r.read.table('webref.txt')

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/joshchang/.sage/sage_notebook/worksheets/admin/1/code/
6.py", line 4, in <module>
r.read.table(\u0027webref.txt\u0027)
File "/Applications/sage/local/lib/python2.5/site-packages/sympy/
plotting/", line 1, in <module>

File "/Applications/sage/local/lib/python2.5/site-packages/rpy.py",
line 302, in __getattr__
return self.__getitem__(name)
File "/Applications/sage/local/lib/python2.5/site-packages/rpy.py",
line 306, in __getitem__
obj = self.__dict__[name] = self.__dict__.get(name,
self.get(name))
rpy.RPy_RException: Error in function (x, pos = -1, envir =
as.environment(pos), mode = "any", :
variable "read" was not found

or using scan

r.scan('webref.txt',sep=" ")

Warning message:
In file(file, "r") :
cannot open file 'webref.txt', reason 'No such file or directory'
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Users/joshchang/.sage/sage_notebook/worksheets/admin/1/code/7.py",
line 4, in <module>
exec compile(ur'r.scan(\u0027webref.txt\u0027,sep=" ")' + '\n',
'',
'single')
File
"/Applications/sage/local/lib/python2.5/site-packages/sympy/
plotting/",
line 1, in <module>

rpy.RPy_RException: Error in file(file, "r") : unable to open
connection


More generally, how can I read data from a file into the sage
interface itself and have the data stored as a matrix?

Thanks in advance.

[Pizzalova]

Ok I figured out why R wasn't finding the data, I had to add ../../ to
the beginning of the file name since each cell is a directory it
seems. Will the R interpreter ever work by selecting the interpreter
without having to append r. to the beginning of each command? Any word
on getting plots to display inline?

[Jacob Hicks]

Plots can be displayed inline in the notebook. Any image sent to
os.curdir gets displayed in the notebook. So all you have to do is
tell r to send its images there.
This is an example plotting with r to the notebook.

from rpy import r
r.png(os.curdir+'/sage.png')

r.par(ann=0)
values = [x for x in srange(0,float(pi),.1)]
r.plot(values, [cos(x^2) for x in values], type='l')
_ = r.dev_off()

Jacob

[William Stein]

To avoid potential frustration, I just want to note that I tried
this on my OS X laptop and it does _not_ work:

{{{id=141|

from rpy import r
r.png(os.curdir+'/sage.png')

r.par(ann=0)
values = [x for x in srange(0,float(pi),.1)]
r.plot(values, [cos(x^2) for x in values], type='l')
_ = r.dev_off()

///
print "\x01r\x01e327"
Warning message:
In function (filename = "Rplot%03d.png", width = 480, height = 480, :
unable to open connection to X11 display ''

Traceback (most recent call last):

rpy.RPy_RException: Error in X11(paste("png::", filename, sep = ""),
width, height, pointsize, :
unable to start device PNG
}}}

[Jacob Hicks]

Does this means that the only output of plotting R supports in sage
instances that aren't compiled from source on a Linux machine with X
development libraries installed is to .ps files? I knew that was true
for source installs of sage. I haven't ever used the binaries of
sage, but it seems they could have the potential to support png output
from R if they were compiled on a machine with the needed libraries.

--
Jacob Hicks
Mathematics Teacher
Trinity Collegiate School

[William Stein]

On Feb 7, 2008 4:27 AM, Jacob Hicks <jacob....@gmail.com> wrote:
>
> Does this means that the only output of plotting R supports in sage
> instances that aren't compiled from source on a Linux machine with X
> development libraries installed is to .ps files?

Yes, that's true.

> I knew that was true
> for source installs of sage. I haven't ever used the binaries of
> sage, but it seems they could have the potential to support png output
> from R if they were compiled on a machine with the needed libraries.

They are built on fairly minimal machines, so that they will actually work.

Anyway, I hope an R expert such as you will improve matters regarding
R graphics in Sage. Send us patches, etc.!

--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

[Pizzalova]

Compiling sage from source and then invoking sage within xterm seem to
make R detect libpng and X11. It seems that the binaries that are
provided were compiled on a mac without the X development headers in
place.

Back to the original topic, I found that I could get to the data using
the built in DATA variable open(DATA+'source.txt') to open source.txt.

source.txt is a 2 column tab delimited file, how can I load it into a
matrix or whatever python object and do a quick and dirty scatter plot
of it without invoking R? Sorry, I'm a complete python newb, and I'm
googling for a solution right now.

Thanks in advance.

On Feb 7, 10:54 am, "William Stein" <wst...@gmail.com> wrote:

> On Feb 7, 2008 4:27 AM, Jacob Hicks <jacob.m.hi...@gmail.com> wrote:
>
>
>
> > Does this means that the only output of plotting R supports in sage
> > instances that aren't compiled from source on a Linux machine with X
> > development libraries installed is to .ps files?
>
> Yes, that's true.
>
> >  I knew that was true
> > for source installs of sage.  I haven't ever used the binaries of
> > sage, but it seems they could have the potential to support png output
> > from R if they were compiled on a machine with the needed libraries.
>
> They are built on fairly minimal machines, so that they will actually work.
>
> Anyway, I hope an R expert such as you will improve matters regarding
> R graphics in Sage.  Send us patches, etc.!
>
>
>
>
>
> > On Feb 6, 2008 6:10 PM, William Stein <wst...@gmail.com> wrote:
>

[shahab]

Many of the SAGE binaries are built without X11 option turned on (b/c
of the missing development headers).
For a quick fix without rebuilding SAGE, one can use the following:

Another option for having R display its graphics in the notebook is to
use an X11 independent rendering of jpeg/png/gif images.

1) Install the sage experimental package 'gd-2.0.34'

install_package('gd-2.0.34')

2) Install the R package GDD

From the notebook session:
from rpy import *
r("install.packages(('GDD'),,'http://www.rosuda.org/R')")

3) That's it.
Run the following example:

r.library("GDD")
r.GDD("demo", type = "png", width=800, height=600)
r.par(ann=0)
values = [x for x in srange(0,float(pi),.01)]

r.plot(values, [cos(x^2) for x in values], type='l')

r.dev_off()

Here is the link to the GDD package:
http://cran.r-project.org/doc/packages/GDD.pdf

Shahab

[Michael Abshoff]

shahab wrote:
>
> Many of the SAGE binaries are built without X11 option turned on (b/c
> of the missing development headers).
> For a quick fix without rebuilding SAGE, one can use the following:
>
> Another option for having R display its graphics in the notebook is to
> use an X11 independent rendering of jpeg/png/gif images.

That sounds definitely like something that should be done once we do more
work on a tighter integration between Sage and R.

> 1) Install the sage experimental package 'gd-2.0.34'

Any reason the current gd-2.0.35.p2 doesn't work? We are planning to
update to 2.0.36 anyway, I am just curious.

> install_package('gd-2.0.34')
>
> 2) Install the R package GDD
>
> From the notebook session:
> from rpy import *
> r("install.packages(('GDD'),,'http://www.rosuda.org/R')")
>
> 3) That's it.
> Run the following example:
>
> r.library("GDD")
> r.GDD("demo", type = "png", width=800, height=600)
> r.par(ann=0)
> values = [x for x in srange(0,float(pi),.01)]
> r.plot(values, [cos(x^2) for x in values], type='l')
> r.dev_off()
>
> Here is the link to the GDD package:
> http://cran.r-project.org/doc/packages/GDD.pdf
>
> Shahab

I think we should at least open a wishlist ticket for the above solution.
Depending on how large the GDD package for R is we might even do that per
default.

Cheers,

Michael

[shahab]

I think I missed the fact that gd-2.0.35.p2 was part of the standard
packages in SAGE. It should work just fine.

Shahab

On Feb 11, 5:56 am, "Michael Abshoff"
<Michael.Absh...@fsmath.mathematik.uni-dortmund.de> wrote:
> shahabwrote: