Passing python objects to R functions in rpy2

Question

I'm working in a Jupyter notebook with Python 2 and want to use rpy2 to plot a heatmap.

import numpy as np
from rpy2 import robjects
from rpy2.robjects import r, pandas2ri
from rpy2.robjects import Formula, Environment
from rpy2.robjects.vectors import IntVector, FloatVector
from rpy2.robjects.lib import grid
from rpy2.robjects.packages import importr, data
from rpy2.rinterface import RRuntimeError
import warnings


a = np.array([1.5,2.3])
b = np.array([4.2,5.1])
c = np.array([[0.3, 0.6],[0.6, 0.3]])

r.image.plot(a,b,c)

gives me the error

AttributeError: 'SignatureTranslatedFunction' object has no attribute 'plot'

How do I properly pass the parameters into this function? Specs: rpy2 2.5.6 with R3.3.3 and Python 2.7

erocoar · Accepted Answer · 2018-01-31 17:14:22Z

2

That doesn't work because image.plot apparently comes from the package fields. Using image from base R's graphics library, do e.g. this:

import numpy as np
from rpy2.robjects.packages import importr
from rpy2.rinterface import RRuntimeError
import rpy2.robjects.numpy2ri
from IPython.display import Image, display
from rpy2.robjects.lib import grdevices

rpy2.robjects.numpy2ri.activate()
grf = importr('graphics')

a = np.array([1.5,2.3])
b = np.array([4.2,5.1])
c = np.array([[0.3, 0.6],[0.6, 0.3]])

with grdevices.render_to_bytesio(grdevices.png, width=1024, height=896, res=150) as img:
    grf.image(a, b, c)
display(Image(data=img.getvalue(), format='png', embed=True))

gives

To use image.plot, you'd have to run

fields = importr('fields')

and replace grf.image(a, b, c) with fields.image.plot(a, b, c)

edited Jan 31, 2018 at 17:14

answered Jan 31, 2018 at 12:25

erocoar

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9 Comments

user217285 Over a year ago

Thanks for the response! I can't run "from rpy2.robjects.lib import grdevices" though, it says "ImportError: cannot import name grdevices." However, I can run 'grdevices = importr('grDevices')" but it doesn't have the "render_to_bytesio" function you used. I am using rpy2 2.5.6 with R3.3.3 and Python 2.7

user217285 Over a year ago

In fact it's telling me that "rpy2.robjects.lib" can only be completed with "grid" -- I'm not sure what grid even is

erocoar Over a year ago

what exactly does the message say? grid is an R-package!

user217285 Over a year ago

The message says "ImportError: cannot import name grdevices."

user217285 Over a year ago

But I definitely have more R packages (like fields!)

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