Jupyter making 3D matplotlib graphs extremely smal

Question

Having read many of the posts on this site about resizing graphs and setting limits on graph sizes in Jupyter, I am virtually convinced there is something different when it comes to 3D plotting.

This is my 3D scatterplot that Jupyter keeps giving back to me, despite having tried many figsize and dpi= settings (either in plt.figure() or within plt.rcParams()),

This is my data and my current code,

%pylab inline
pylab.rcParams['figure.figsize'] = (20, 16)
pylab.rcParams['figure.dpi'] = 200

import matplotlib.pyplot as plt
import matplotlib

from mpl_toolkits.mplot3d import Axes3D

# data1

fig = plt.figure()

ax = fig.add_subplot(111, projection='3d')

ax.scatter(data1.a_close, data1.g_close, data1.m_close)

What am I doing wrong?

EDIT: I am using a Mac (10.11) and these are all my pip installed packages, if this provides some detail. I also tried uninstalling and reinstalling jupyter, but that has not helped

alabaster==0.7.12
anaconda-client==1.6.14
anaconda-navigator==1.8.7
anaconda-project==0.8.2
appnope==0.1.0
appscript==1.0.1
argh==0.26.2
asn1crypto==0.24.0
astroid==2.0.4
astropy==3.0.5
atomicwrites==1.2.1
attrs==18.2.0
Babel==2.6.0
backcall==0.1.0
backports.shutil-get-terminal-size==1.0.0
beautifulsoup4==4.6.3
bitarray==0.8.3
bkcharts==0.2
blaze==0.11.3
bleach==3.0.2
blist==1.3.6
bokeh==1.0.0
boto==2.48.0
Bottleneck==1.2.1
certifi==2018.4.16
cffi==1.11.5
chardet==3.0.4
Click==7.0
cloudpickle==0.6.1
clyent==1.2.2
colorama==0.4.0
conda==4.5.9
conda-build==3.0.27
conda-verify==2.0.0
contextlib2==0.5.5
cryptography==2.3.1
CVXcanon==0.1.1
cvxopt==1.2.2
cvxpy==1.0.10
cycler==0.10.0
Cython==0.29
cytoolz==0.9.0.1
dash==0.28.5
dash-core-components==0.35.2
dash-html-components==0.13.2
dash-renderer==0.14.3
dash-table-experiments==0.6.0
dask==0.19.4
datashape==0.5.4
decorator==4.3.0
defusedxml==0.5.0
dill==0.2.8.2
distcan==0.0.1
distributed==1.23.3
Django==2.1.2
docutils==0.14
ecos==2.0.5
entrypoints==0.2.3
et-xmlfile==1.0.1
eventsourcing==6.3.0
fastcache==1.0.2
fastnumbers==2.1.1
feather-format==0.4.0
filelock==3.0.9
fix-yahoo-finance==0.0.22
Flask==1.0.2
Flask-Caching==1.4.0
Flask-Compress==1.4.0
Flask-Cors==3.0.6
future==0.16.0
gevent==1.3.7
glmnet==2.0.0
glmnet-py==0.1.0b2
glob2==0.6
gmpy2==2.0.8
greenlet==0.4.15
h5py==2.8.0
heapdict==1.0.0
html5lib==1.0.1
hupper==1.3.1
idna==2.7
imageio==2.4.1
imagesize==1.1.0
importlib-metadata==0.6
inflection==0.3.1
ipykernel==5.1.0
ipython==7.0.1
ipython-genutils==0.2.0
ipywidgets==7.4.2
isort==4.3.4
ItsDangerous==1.0.0
jdcal==1.4
jedi==0.13.1
Jinja2==2.10
joblib==0.12.5
jsonschema==2.6.0
jupyter==1.0.0
jupyter-client==5.2.3
jupyter-console==6.0.0
jupyter-core==4.4.0
jupyterlab==0.35.2
jupyterlab-launcher==0.13.1
jupyterlab-server==0.2.0
keyring==15.1.0
kiwisolver==1.0.1
lazy-object-proxy==1.3.1
llvmlite==0.25.0
locket==0.2.0
lxml==4.2.5
Markdown==3.0.1
MarkupSafe==1.0
matplotlib==3.0.0
mccabe==0.6.1
mistune==0.8.4
mizani==0.5.2
mlxtend==0.13.0
mock==2.0.0
more-itertools==4.3.0
mpmath==1.0.0
msgpack==0.5.6
msgpack-python==0.5.6
multipledispatch==0.6.0
multiprocess==0.70.6.1
multitasking==0.0.7
natsort==5.4.1
navigator-updater==0.2.1
nbconvert==5.4.0
nbformat==4.4.0
ndg-httpsclient==0.5.1
networkx==2.2
nltk==3.3
nose==1.3.7
notebook==5.7.0
numba==0.40.1
numexpr==2.6.8
numpy==1.15.3
numpydoc==0.8.0
odo==0.5.1
olefile==0.46
openpyxl==2.5.9
osqp==0.4.1
packaging==18.0
palettable==3.1.1
pandas==0.23.4
pandas-datareader==0.7.0
pandocfilters==1.4.2
parso==0.3.1
partd==0.3.9
PasteDeploy==1.5.2
path.py==11.5.0
pathlib2==2.3.2
patsy==0.5.0
pbr==5.1.0
pep8==1.7.1
pexpect==4.6.0
pickleshare==0.7.5
Pillow==5.3.0
pkginfo==1.4.2
plaster==1.0
plaster-pastedeploy==0.6
plotly==3.3.0
pluggy==0.8.0
ply==3.11
prometheus-client==0.4.2
prompt-toolkit==2.0.6
psutil==5.4.7
ptyprocess==0.5.2
py==1.7.0
pyarrow==0.11.1
pyasn1==0.4.4
pycodestyle==2.4.0
pycosat==0.6.3
pycparser==2.19
pycrypto==2.6.1
pycryptodome==3.6.6
pycurl==7.43.0.2
pyflakes==2.0.0
Pygments==2.2.0
pylint==2.1.1
pymc3==3.5
pyodbc==4.0.24
pyOpenSSL==18.0.0
pyparsing==2.2.2
PyQt5==5.11.3
PyQt5-sip==4.19.13
pyramid-arima==0.8.1
PySocks==1.6.8
pystan==2.18.0.0
pytest==3.9.2
python-dateutil==2.7.3
pytz==2018.6
PyWavelets==1.0.1
PyYAML==3.12
pyzmq==17.1.2
qfrm==0.2.0.27
QtAwesome==0.5.1
qtconsole==4.3.1
QtPy==1.5.2
Quandl==3.4.3
redis==2.10.6
repoze.lru==0.7
requests==2.20.0
requests-file==1.4.3
requests-ftp==0.3.1
retrying==1.3.3
rope==0.11.0
rpy2==2.9.4
ruamel-yaml==0.11.14
scikit-image==0.14.1
scikit-learn==0.19.0
scipy==1.1.0
scs==2.0.2
seaborn==0.9.0
Send2Trash==1.5.0
simplegeneric==0.8.1
simplejson==3.16.0
singledispatch==3.4.0.3
sip==4.19.8
six==1.11.0
snowballstemmer==1.2.1
sortedcollections==1.0.1
sortedcontainers==2.0.5
Sphinx==1.8.1
sphinxcontrib-websupport==1.1.0
spyder==3.3.1
spyder-kernels==1.1.0
SQLAlchemy==1.2.12
statistics==1.0.3.5
statsmodels==0.9.0
sympy==1.1.1
tables==3.4.4
tblib==1.3.2
terminado==0.8.1
testpath==0.4.2
Theano==1.0.3
toolz==0.9.0
tornado==5.1.1
tqdm==4.28.1
traitlets==4.3.2
translationstring==1.3
typed-ast==1.1.0
typing==3.6.6
tzlocal==1.5.1
unicodecsv==0.14.1
urllib3==1.24
venusian==1.1.0
wcwidth==0.1.7
webencodings==0.5.1
WebOb==1.8.3
Werkzeug==0.14.1
widgetsnbextension==3.4.2
wrapt==1.10.11
xlrd==1.1.0
XlsxWriter==1.1.2
xlwings==0.13.0
xlwt==1.3.0
yahoo-finance==1.4.0
zict==0.1.3
zope.deprecation==4.3.0
zope.interface==4.6.0

Answer 1

This is due to a bug in matplotlib 3.0.0. It should not occur in matplotlib 3.0.1.

Options you have:

• Update to matplotlib 3.0.1

• Set the following option in your jupyter notebook before plotting

  %config InlineBackend.print_figure_kwargs = {'bbox_inches':None}
  

• Use the %matplotlib notebook backend instead of the %matplotlib inline one.

Answer 2

Try replacing

%pylab inline
pylab.rcParams['figure.figsize'] = (20, 16)
pylab.rcParams['figure.dpi'] = 200

import matplotlib.pyplot as plt
import matplotlib

with

%matplotlib inline

import matplotlib.pyplot as plt
import matplotlib

matplotlib.rcParams['figure.figsize'] = (20, 16)
matplotlib.rcParams['figure.dpi'] = 200

Answer 3

Sometimes that happens to me as well on my Mac.

First use this:

import matplotlib.pyplot as plt
import matplotlib
%matplotlib inline

matplotlib.rcParams['figure.figsize'] = (20, 16)
matplotlib.rcParams['figure.dpi'] = 200

The trick for my case: First import and then use the %matplotlib inline command. However, seems like a bug.