Interactive work¶
Overview¶
R is very often used as an interactive toplevel, or read-eval-print loop (REPL). When analyzing data this is kind of environment is extremely convenient as the analyst often does not know beforehand what lies in the data and how this is going to be discovered.
Python is can also be used in a similar fashion, but limitations of the default Python console have lead to the creation of alternative consoles and interactive development editors (idle, ipython, bpython, emacs mode, komodo, ...). Features such as code highlighting, autocompletion, and convenient display of help strings or function signatures have made those valuable tools.
The package rpy2.interactive aims at interactive users, but can be used in non-interactive code as well. It is trading trading flexibility or performances for ease-of-use.
>>> import rpy2.interactive as r
>>> v = r.IntVector((1,2,3))
>>> r.importr('datasets')
rpy2.robjecs.packages.Package as a <module 'datasets' (built-in)>
>>> tuple(r.packages.datasets.trees.names)
('Girth', 'Height', 'Volume')
R vectors¶
>>> import rpy2.interactive as r
>>> r.IntVector(range(10))
<IntVector - Python:0x935774c / R:0xa22b440>
[ 0, 1, 2, ..., 7, 8, 9]
>>> r.IntVector(range(100))
<IntVector - Python:0xa1c2dcc / R:0x9ac5540>
[ 0, 1, 2, ..., 97, 98, 99]
In R, there are no scalars.
>>> r.packages.base.pi
<FloatVector - Python:0xa1d7a0c / R:0x9de02a8>
[3.141593]
To know more, please check Section R vectors.
R packages¶
R has a rich selection of packages, known in other computer languages and systems as libraries.
R Packages can be:
- available in R repositories (public or private)
- installed
- attached (loaded)
Loading installed packages¶
When starting R, the base package as well as by default the packages grDevices, graphics, methods, stats, and utils are loaded.
We start with the loading of R packages since this is a very common operation in R, and since R is typically distributed with recommended packages one can immediately start playing with.
Loading installed R packages can be done through the function importr().
>>> import rpy2.interactive as r
>>> r.importr("cluster")
rpy2.robjecs.packages.Package as a <module 'cluster' (built-in)>
The function returns a package object, and also adds a reference to it in r.packages
>>> r.packages.cluster
rpy2.robjecs.packages.Package as a <module 'cluster' (built-in)>
All objects in the R package cluster can subsequently be accessed through that module-like object. For example, for the function barplot:
>>> r.packages.cluster.silhouette
<SignatureTranslatedFunction - Python:0x24f9418 / R:0x2f5b008>
Similarly, other packages such as nlme, and datasets can be loaded.
>>> r.importr("nlme")
rpy2.robjecs.packages.Package as a <module 'stats' (built-in)>
>>> r.importr("datasets")
rpy2.robjecs.packages.Package as a <module 'datasets' (built-in)>
We can then demonstrate how to access objects in R packages through a graphical example:
r.packages.graphics.coplot(r.Formula('Time ~ conc | Wt'),
r.packages.datasets.Theoph)
Available packages¶
R has a function to check was are the available packages.
Note
To list the available packages, we have to load the package utils. See Section load-packages for details about loading packages
>>> import rpy2.interactive as r
>>> r.importr("utils")
>>> m = r.packages.utils.available_packages()
The object returned is a rpy2.robjects.vectors.Matrix, with one package per row (there are many packages in the default CRAN repository).
>>> tuple(m.dim)
(2692, 13)
>>> tuple(m.colnames)
('Package', 'Version', 'Priority', 'Depends', 'Imports', 'LinkingTo', 'Suggests', 'Enhances', 'OS_type', 'License', 'Archs', 'File', 'Repository')
Note
Specific repositories can be specified.
For example with bioconductor.
import rpy2.rinteractive as r
bioc_rooturl = "http://www.bioconductor.org/packages"
bioc_version = "2.7"
bioc_sections = ("bioc", "data/annotation", "data/experiment", "extra")
repos = r.vectors.StrVector(["/".join((bioc_rooturl, bioc_version, x)) for x in bioc_sections])
m_bioc = r.packages.utils.available_packages(contriburl = r.packages.utils.contrib_url(repos))
Installing packages¶
Note
To install a package for repositories, we have to load the package utils. See Section load-packages for details about loading packages
>>> import rpy2.interactive as r
>>> r.importr("utils")
>>> package_name = "lme4"
>>> r.packages.utils.install_packages(package_name)
Once a package is installed it will be available for future use without having the need to install it again (unless a different version of R is used).
R event loop¶
Code author: Thomas Kluyver, Laurent Gautier
In order to perform operations like refreshing interactive graphical devices, R need to process the events triggering the refresh.
>>> from rpy2.interactive import process_revents
>>> process_revents.start()
>>> from rpy2.robjects.packages import importr
>>> from rpy2.robjects.vectors import IntVector
>>> graphics = importr("graphics")
>>> graphics.barplot(IntVector((1,3,2,5,4)), ylab="Value")
Now the R graphical device is updated when resized. Should one wish to stop processing the events:
>>> process_revents.stop()
The processing can be resumed, stopped again, and this repeated ad libitum.
The frequency with which the processing of R events is performed can be roughly controlled. The thread is put to sleep for an arbitray duration between each processing of R events.
>>> process_revents.EventProcessor.interval
0.2
This value can be changed and set to an other value if more or less frequent processing is wished. This can be done while the threaded processing is active and will be taken into account at the next sleep cycle.
>>> process_revents.EventProcessor.interval = 1.0
- rpy2.interactive.process_revents.process_revents()¶
Process R events. This function is a simple wrapper around R_ProcessEvents (on win32 and MacOS X-Aqua) and R_runHandlers (on other platforms).
