Laurent Gautier lgautier

Data Science, Life Sciences & Healthcare

lgautier / reticulate-from-rpy2.py

Created March 25, 2023 16:24

	Python 3.8.10 (default, Mar 13 2023, 10:26:41)
	Type 'copyright', 'credits' or 'license' for more information
	IPython 8.11.0 -- An enhanced Interactive Python. Type '?' for help.

	In [1]: from rpy2.robjects.packages import importr

	In [2]: reticulate = importr('reticulate')

	WARNING: The R package "reticulate" only fixed recently
	an issue that caused a segfault when used with rpy2:

lgautier / multiproc_lab.py

Created January 3, 2020 23:02

"Lab" to show how to perform parallel R computing using `multiprocessing`.

	import argparse
	import multiprocessing as mp
	import uuid
	import rpy2.rinterface as ri
	import rpy2.rinterface_lib.embedded

	R_ID_TAG = '_rpy2_R_id_'


	def print_setup(args):

lgautier / rpy2-ld-library-path.sh

Created December 31, 2019 17:55

Set LD_LIBRARY_PATH for rpy2 when R is in a non-system location

export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}

lgautier / demo_benchmark_mashingp.sh

Last active January 30, 2017 04:37

Demo/benchmark mashing-pumpkins to build minhash sketches

lgautier / dplyr.ipynb

Last active January 18, 2016 21:00

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lgautier / rpy2_stap_example

Last active August 29, 2015 14:25

	power <- function(x, n) {
	# a not-so-useful reimplementation
	x ^ n
	}

	square <- function(x) {
	x^2
	}

	cube <- function(x) {

lgautier / ipysetup.py

Created December 26, 2014 16:50

Customization of rpy2 (see comments at https://bitbucket.org/rpy2/rpy2/issue/230/rmagic-specific-conversion)

	# This is a setup snippet for an ipython notebook.
	# It requires the presence of variable 'setup_digest',
	# defined in the cell controlling the setup.
	if 'setup_digest' not in locals():
	import rpy2
	%load_ext rpy2.ipython

	# pigheaded / slow rpy2 developpers,
	# customize away:
	from rpy2.robjects.conversion import ri2py

lgautier / rmagic_singledispatch

Last active August 29, 2015 14:08

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	"signature": "sha256:cd75955d68d7ca272ff32886ce865002acb49b25f2e1cfba237539e70925eeda"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [

lgautier / gist:955e14077322480803e2

Created September 30, 2014 02:36

rpy2 and HTML display in ipython

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	"name": "",
	"signature": "sha256:e814b7d85c1dc274b3c62ca6849951326dee84fa31b999f9735064f46fb45a7a"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [

lgautier / gist:5426275

Created April 20, 2013 15:05

ipython notebook (Python 3.3.1, R-3.0.0, rpy2-2.4.0-dev

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