How to set mfrow/mfcol in python

Question

Through rpy2 in jupyter, you may plot your data directly from python using R objects. How can you set par(mfrow=c(1,2) in python?

For instance, I want to automatically feed a matrix with variable size from python and plot it (among other statistical analyses) using rpy2. But instead of plotting a single boxplot, I want all of them to be output.

Here's some sample code

import rpy2.ipython
import rpy2.robjects as ro
import scipy as sp
import re #python for regex
from rpy2.robjects.packages import importr
rpy2.robjects.numpy2ri.activate()
%load_ext rpy2.ipython
%R

test=[[1,3,2],[6,5,7,8,9]]

def funtoanalyze(grouparray):
    a={}
    data=numpy.array(test)
    for ig in range(len(grouparray)):
        key=grouparray[ig]
        value=data[ig]
        a[key]=value
        next
    rbox=ro.r('boxplot')
    for gro in a:    
        datar=a[gro]
        ro.r('dev.new()')
        rbox(ro.FloatVector(datar[:]),xlab="",main=gro)
    return

funtoanalyze(["group33","group2"]) #only plots last group

Answer 1

Your use of %load_ext rpy2.ipython suggests that you want to have your figure in the jupyter notebook.

R is using "graphical devices" to output figures, and calling par(mfrow=c(...)) will either put the setting in an open graphical device or open a new default device and set the parameter.

The "magic" %%R is scanning if figures were generated on default devices and display them in the notebook. The following should work:

%%R

par(mfrow=c(1,2))
plot(0, 0)
plot(0, 0)

If you do not want to use the R magic, there are other utilities for the jupyter notebook in rpy2. For plotting there is a context manager (see https://bitbucket.org/rpy2/rpy2/issues/330/ipython-plotting-wrapper - I don't remember if there is more documentation), but the most advanced utilities are tailored for ggplot2. Check for example this slides and the following ones: https://lgautier.github.io/odsc-ppda-slides/#/5/13

The full notebook is here:

https://github.com/lgautier/odsc-ppda-slides/blob/master/notebooks/slides.ipynb

There is a docker container shipping with everything needed to run the notebook:

https://github.com/lgautier/pragmatic-polyglot-data-analysis