Você precisará do atleast versão 1.2.0 do matplotlib e, em seguida, usar os backends do GTK3.
Exemplo retirado do link
#!/usr/bin/env python
"""
demonstrate adding a FigureCanvasGTK3Agg widget to a Gtk.ScrolledWindow
using GTK3 accessed via pygobject
"""
from gi.repository import Gtk
from matplotlib.figure import Figure
from numpy import arange, sin, pi
from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas
win = Gtk.Window()
win.connect("delete-event", Gtk.main_quit )
win.set_default_size(400,300)
win.set_title("Embedding in GTK")
f = Figure(figsize=(5,4), dpi=100)
a = f.add_subplot(111)
t = arange(0.0,3.0,0.01)
s = sin(2*pi*t)
a.plot(t,s)
sw = Gtk.ScrolledWindow()
win.add (sw)
# A scrolled window border goes outside the scrollbars and viewport
sw.set_border_width (10)
canvas = FigureCanvas(f) # a Gtk.DrawingArea
canvas.set_size_request(800,600)
sw.add_with_viewport (canvas)
win.show_all()
Gtk.main()
Nota: O Ubuntu 12.04 não possui o Matplotlib 1.2.0 no repositório, mas é instalável através de pip
:
sudo pip install matplotlib