/knitron

[DEPRECATED] Use IPython and matplotlib in knitr!

Primary LanguageR

knitron: knitr + IPython + matplotlib

Build Status

Knitron brings the power of IPython and matplotlib to knitr.

It also brings workspace-like interaction for Python to knitr, so you can define a variable in one chunk

x = 5

and access it in a following chunk

x + 1
## 6

Requirements

  • R with knitr and devtools
  • A recent version of IPython (knitron relies on the new IPython.parallel API)
  • pyzmq

These can be installed by executing (in a shell):

Rscript -e "install.packages('knitr')"
apt-get install python-dev libzmq3-dev libgit2-dev # on Debian and derivates
Rscript -e "install.packages('devtools')"
pip install IPython
pip install pyzmq

In even newer version of IPython, the parallel API has been split in a separate package, usually called ipyparallel:

pip install ipyparallel

Installation

In R:

library(devtools)
install_github("knitron", "fhirschmann")

Design

In order to provide a persistent state for multiple chunks in a document, knitron makes use of IPython's architecture for parallel computing. An IPython cluster is started into the background before the chunks are being processed.

Usage

library(knitron)

That's it! Now you can use IPython in knitr using the engine = 'ipython' option (see the source code of this page for an example).

By default, the knitr IPython profile will be used. You can change this using the knitron.profile chunk option. If the profile doesn't exist already, it will be created and can then be modified (take a look at ~/.ipython/profile_knitr). When the first chunk for each profile gets evaluated, a cluster with one engine will be spawned by knitron if it isn't already running. You can also spawn your cluster in a parallel process using

ipcluster start --profile=knitr --n=1

If the cluster has been spawned by knitron, it will be terminated on exit.

RStudio Usage

To use knitron in RStudio, the knitron library needs to be loaded in an R chunk. This can usually be done in the preamble, i.e. for LaTeX before executing any IPython chunk, define:

<<setup, echo = F>>=
library(knitron)
@

An exemplary document showing the use of knitron inside RStudio is available.

Matplotlib

Knitron imports matplotlib and pyplot (as plt) unless knitron.matplotlib is set to FALSE. For figures to appear after the chunk, pyplot is expected to be used.

Chunk Options

The following knitron-specific chunk options are available in knitron:

  • knitron.profile = "knitr" specifies the IPython profile to be used for the evaluation of the chunk.
  • knitron.matplotlib = TRUE loads matplotlib and pyplot (as plt) before executing a chunk.
  • knitron.print = "auto" will print the string representation of the last object in a code chunk. By default, it will not print the string representation of a plot. Other values for this option are TRUE and FALSE.

Supported Features and Limitations

Most of the original knitr chunk options are supported, including

  • fig.path
  • fig.width and fig.height
  • dpi
  • dev 'pdf' for LaTeX and 'png' for HTML/markdown; most of the other devices (e.g. svg, Cairo_png) are supported too

However, there are limitations to some options:

  • fig.show only supports hold, i.e. all figures are placed at the end of each code chunk
  • dev currently supports only one device per chunk, i.e. you cannot give a character vector so that two plots with different devices are generated

IPython's magic functions are supported too, of course. But there are some limitations, i.e. magic functions that insert text into the IPython shell like %load without executing them don't work. Likewise, magics that are meant for interactive use like %man and %edit cannot work in knitr.

Examples

IPython

from time import sleep

%time sleep(0.5)
## CPU times: user 0 ns, sys: 0 ns, total: 0 ns
## Wall time: 500 ms

%whos
## Variable     Type                          Data/Info
## ----------------------------------------------------
## f            function                      <function f at 0x7f504addf140>
## matplotlib   module                        <module 'matplotlib' from<...>matplotlib/__init__.pyc'>
## np           module                        <module 'numpy' from '/us<...>ages/numpy/__init__.pyc'>
## plt          module                        <module 'matplotlib.pyplo<...>s/matplotlib/pyplot.pyc'>
## sleep        builtin_function_or_method    <built-in function sleep>
## t1           ndarray                       50: 50 elems, type `float64`, 400 bytes
## t2           ndarray                       250: 250 elems, type `float64`, 2000 bytes
## x            int                           5

Matplotlib

import numpy as np
x = np.linspace(0, 2 * np.pi, 100)
y1 = np.sin(x)
y2 = np.sin(3 * x)
plt.fill(x, y1, 'b', x, y2, 'r', alpha=0.3)

plot of chunk example1

L = 6
x = np.linspace(0, L)
ncolors = len(plt.rcParams['axes.color_cycle'])
shift = np.linspace(0, L, ncolors, endpoint=False)
for s in shift:
    plt.plot(x, np.sin(x + s), 'o-')
## /usr/lib/python2.7/dist-packages/matplotlib/__init__.py:894: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
##   warnings.warn(self.msg_depr % (key, alt_key))

plot of chunk example2