olgabot / prettyplotlib Goto Github PK

ImportError Traceback (most recent call last)
in ()
----> 1 import prettyplotlib

C:\Users\Feng\build\bdist.win-amd64\egg\prettyplotlib__init__.py in ()

C:\Users\Feng\build\bdist.win-amd64\egg\prettyplotlib_bar.py in ()

C:\Users\Feng\build\bdist.win-amd64\egg\prettyplotlib\utils.py in ()

D:\Python\Python27\lib\site-packages\matplotlib\pyplot.py in ()
22
23 import matplotlib
---> 24 import matplotlib.colorbar
25 from matplotlib import _pylab_helpers, interactive
26 from matplotlib.cbook import dedent, silent_list, is_string_like, is_numlike

D:\Python\Python27\lib\site-packages\matplotlib\colorbar.py in ()
27 import matplotlib.artist as martist
28 import matplotlib.cbook as cbook
---> 29 import matplotlib.collections as collections
30 import matplotlib.colors as colors
31 import matplotlib.contour as contour

D:\Python\Python27\lib\site-packages\matplotlib\collections.py in ()
21 import matplotlib.artist as artist
22 from matplotlib.artist import allow_rasterization
---> 23 import matplotlib.backend_bases as backend_bases
24 import matplotlib.path as mpath
25 from matplotlib import _path

D:\Python\Python27\lib\site-packages\matplotlib\backend_bases.py in ()
48
49 import matplotlib.tight_bbox as tight_bbox
---> 50 import matplotlib.textpath as textpath
51 from matplotlib.path import Path
52 from matplotlib.cbook import mplDeprecation

D:\Python\Python27\lib\site-packages\matplotlib\textpath.py in ()
9 from matplotlib.path import Path
10 from matplotlib import rcParams
---> 11 import matplotlib.font_manager as font_manager
12 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING
13 from matplotlib.ft2font import LOAD_TARGET_LIGHT

D:\Python\Python27\lib\site-packages\matplotlib\font_manager.py in ()
51 import matplotlib
52 from matplotlib import afm
---> 53 from matplotlib import ft2font
54 from matplotlib import rcParams, get_cachedir
55 from matplotlib.cbook import is_string_like

ImportError: numpy.core.multiarray failed to import

Sadly this seems to be missing :(

When I try using the remove_chartjunk method for getting rid of axes plus BOTH ticklabels, that is

ppl.utils.remove_chartjunk(ax, ['top', 'right', 'left', 'bottom'], ticklabels=['x', 'y'])

only the x-axis ticklabels are suppressed. Same happens if I swap the axes, e.g. ticklabels=['y', 'x']. Looking at the code, the issue seems to reside in a misused elif statement.

I've modified bar and barh charts to support stacking and annotating stack values for my personal project. I can issue a pull request if you are interested in adding this support for bar charts.

Is there a reason why caps have been reintroduced in boxplot?
Suggestion for line 91:
plt.setp(bp['caps'], color='white')

Here is an example of what I am trying to do:

import prettyplotlib as ppl
import matplotlib.pyplot as plt
import numpy as np

x = 5 + np.linspace(-np.pi, np.pi, 100)
y = 2 + np.linspace(0, 2*np.pi, 100)

X, Y = np.meshgrid(x, y)
C = np.tanh(X) + np.cos(Y)

fig, ax = plt.subplots(1)
ppl.pcolormesh(fig, ax, X, Y, C)
#ax.axis('image')

but ppl does not accept the standard pcolormesh arguments (https://github.com/olgabot/prettyplotlib/blob/master/prettyplotlib/_pcolormesh.py#L34)

I can see fixing it by checking if the first three arguments are of type np.ndarray, and if so, using the third on as x. Or, by having a kwarg like Qx and Qy that contains the coordinates to plot against, then pass those arrays to pcolormesh like normal.

I just installed prettyplotlib under python3 and I got :

Installing collected packages: prettyplotlib
  Running setup.py install for prettyplotlib
      File "/usr/lib/python3.3/site-packages/prettyplotlib/utils.py", line 125
        print 'len(args) == 0'
                             ^
    SyntaxError: invalid syntax


    warning: manifest_maker: MANIFEST.in, line 3: 'recursive-include' expects <dir> <pattern1> <pattern2> ...

Successfully installed prettyplotlib
Cleaning up...

import prettyplotlib as ppl
import matplotlib.pyplot as plt
import numpy as np

fig, ax = ppl.subplots(1)
np.random.seed(10)
x = np.linspace(-1000,1000,10)
y = np.linspace(-1,1,80)
z = np.random.random([10,80])
X,Y = np.meshgrid(x,y)
ppl.pcolormesh(fig,ax,x,y,z.T)
plt.show()

I would have expected that ppl uses x,y,and z.T as args and then utilizes the pcolormesh(X, Y, C) instead of pcolormesh(C, **kwargs), but it seems as if this is not the case! When I look into the code of ppl.pcolormesh I do not see why this is case!

Your default plot apparently plots the axes but not the tick marks, but Tufte suggests plotting the tick marks but not the axes (or at least making the axes light gray), since the tick marks are data and the axes are just a box that serves little or no information-conveying purpose.

I'm curious as to why you did the opposite of what Tufte suggests here.

If I try to plot something in a pcolormesh plot with prettyplottlib in an IPython notebook, the plot is shown twice. I am plotting figures inline in the notebook and this behaviour occurs both if I start the notebook as:

ipython notebook --matplotlib=inline

Or if I include it via a %matplotlib magic inside the notebook. Example:

%matplotlib inline
import prettyplotlib as ppl
import numpy as np

data = np.random.random((10,10))
ppl.pcolormesh(data)

by default histograms and scatterplots are have edges that are black. This is not pretty. Set edgecolor='none' by default to make this prettier

It looks like with matplotlib 1.3.1 plotting doesn't pick up the right colors.

numpy==1.7.1
prettyplotlib==0.1.7
brewer2mpl==1.4
matplotlib==1.3.1

I'm looking at the example from https://github.com/olgabot/prettyplotlib/wiki/Examples-with-code#plot-lines-eg-time-series-with-a-legend

import prettyplotlib as ppl
import numpy as np

# prettyplotlib imports 
import matplotlib.pyplot as plt
import matplotlib as mpl
from prettyplotlib import brewer2mpl

# Set the random seed for consistency
np.random.seed(12)

fig, ax = plt.subplots(1)

# Show the whole color range
for i in range(8):
    y = np.random.normal(size=1000).cumsum()
    x = np.arange(1000)

    # For now, you need to specify both x and y :(
    # Still figuring out how to specify just one
    ppl.plot(ax, x, y, label=str(i), linewidth=0.75)

ppl.legend(ax)

fig.savefig('plot_prettyplotlib_default.png')

Creates the following image:

If so how please.
Thank you!

This is what I got from the installation through pip (and easy_install):

g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/src/ft2font.o build/temp.linux-x86_64-2.7/src/mplutils.o build/temp.linux-x86_64-2.7/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-2.7/CXX/cxx_extensions.o build/temp.linux-x86_64-2.7/CXX/cxxsupport.o build/temp.linux-x86_64-2.7/CXX/cxxextensions.o -L/usr/local/lib -lfreetype -lstdc++ -lm -o build/lib.linux-x86_64-2.7/matplotlib/ft2font.so

building 'matplotlib._png' extension

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC ->DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib__png_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/python2.7 -c src/_png.cpp -o build/temp.linux-x86_64-2.7/src/_png.o

src/_png.cpp:10:20: fatal error: png.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

Rolling back uninstall of matplotlib
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;file='/tmp/pip_build_root/matplotlib/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-U3hamL-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/matplotlib
Storing debug log for failure in /home/hsuch/.pip/pip.log

I tried to look for png.h, and it looks like it is indeed missing in the downloaded tarball

Not sure why this is happening.. used python setup.py sdist upload to send to PyPI, which did upload a source version, but that isn't getting pulled down by certain users for some reason.

Installation with pip leads to an error:

$ pip install --upgrade prettyplotlib
Downloading/unpacking prettyplotlib from https://pypi.python.org/packages/source/p/prettyplotlib/prettyplotlib-0.1.5.tar.gz#md5=4de2eccf22f1bb8c52b07114d18182dd
  Downloading prettyplotlib-0.1.5.tar.gz (697kB): 697kB downloaded
  Running setup.py (path:/home/jgosmann/.virtualenvs/default/build/prettyplotlib/setup.py) egg_info for package prettyplotlib
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/home/jgosmann/.virtualenvs/default/build/prettyplotlib/setup.py", line 10, in <module>
        LONG_DESCRIPTION = open('README.rst').read()
    IOError: [Errno 2] No such file or directory: 'README.rst'
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/home/jgosmann/.virtualenvs/default/build/prettyplotlib/setup.py", line 10, in <module>

    LONG_DESCRIPTION = open('README.rst').read()

IOError: [Errno 2] No such file or directory: 'README.rst'

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /home/jgosmann/.virtualenvs/default/build/prettyplotlib
Storing debug log for failure in /home/jgosmann/.pip/pip.log

README.rst is indeed missing in the archive being downloaded.

Hi there,

As the title suggests, there is a minor typo in the setup.py file (line 13):

if sys.version_info[0] == 3:
    REQUIREMENTS = open('requirments.txt', encoding='utf-8').readlines()

Try e.g.

import numpy as np, matplotlib.pyplot as plt, prettyplotlib as ppl
f, (ax1, ax2) = plt.subplots(2)
ppl.hist(ax1, np.random.normal(size=(1e6,)), 500)
ax2.hist(np.random.normal(size=(1e6,)), 500)
plt.show()

I guess that the bars become totally invisible because they become thinner than the amount of whitespace ppl is trying to insert between them.

Please add support for plt.errobar.

Is it possible to use prettyplotlib to pretty up the output of dataframe.plot? I tried doing this

with ppl.pretty:
    dataframe.plot()

The resulting plot had the ppl colors but all of the other chart junk, gridlines, etc were the same as the default.

need to change the following:

•  "               edgecolor=ppl.almost_black,\n",
  

•  "               edgecolor=ppl.colors.almost_black,\n",
  

  "import matplotlib.pyplot as plt\n",

•  "    ppl.remove_chartjunk(ax, ['top', 'right'])\n",
  

•  "    ppl.utils.remove_chartjunk(ax, ['top', 'right'])\n",
  

Hi,

Please add support for the easy creation of pretty pie charts.
Ideally for pie charts which could have more than 11 slices*.

Regards,
Sibin

* The maximum number of defined colors for any 'color map' of any 'color map type' is 11 ('Diverging' color map type supports 11 colors).

For a category, if there are equal values, space them apart equally.

I see no images in the comparison with matplotlib.

Currently only importing prettyplolib will change mpl.rcParams defaults, so the following plots, even ones which were not produced with prettyplolib will have different defaults.

import matplotlib.pyplot as plt
from pandas import *
from numpy.random import randn

ts = Series(randn(1000), index=date_range('1/1/2000', periods=1000))
ts = ts.cumsum()

# plots normal plots
ts.plot()
plt.show() 
import prettyplotlib
# plots changed plots
ts.plot()
plt.show() 

[Edit: included example directly]

It would be nice if prettyplotlib would offer two ways to get the new defaults:

• as an rc_context manager
• as an explicit function, which sets this defaults

This would make it easier to use prettyplotlib in libraries

I have a notebook started with --pylab inline and a script that looks like this:

import prettyplotlib as ppl

np.random.seed(12)

fig, ax = plt.subplots(1)

ppl.hist(ax, np.random.randn(1000))

But the output seems to render using the default matplotlib colours:

Am I doing something wrong, or is there a version incompatibility somewhere?

This is on Ubuntu 12.04, Python 3.4, and here is the output of pip --list:

beautifulsoup4 (4.2.1)
Bottleneck (0.8.0)
brewer2mpl (1.4)
Cython (0.20.1)
deap (1.0.1)
distribute (0.6.49)
docutils (0.11)
fastcluster (1.1.13)
ipython (2.0.0)
Jinja2 (2.7.2)
lxml (3.3.5)
MarkupSafe (0.21)
matplotlib (1.3.1)
nose (1.3.1)
numexpr (2.4)
numpy (1.8.1)
numpydoc (0.5.dev)
pandas (0.13.1)
patsy (0.2.1)
pip (1.5.4)
prettyplotlib (0.1.7)
psycopg2 (2.5.2)
Pygments (1.6)
pymc (3.0)
pyparsing (2.0.2)
python-dateutil (2.2)
pytz (2014.2)
pyzmq (14.1.1)
scikit-learn (0.15-git)
scipy (0.13.3)
seaborn (0.3)
setuptools (0.6c11)
six (1.6.1)
Sphinx (1.2.2)
statsmodels (0.6.0)
sympy (0.7.5)
tables (3.1.1)
Theano (0.6.0)
tornado (3.2)

When I create a histogram with a log scale, the y-axis is too large to show the available data. If I add a limit using ax.set_ylim(0, 25), the graph still does not show any data.

import prettyplotlib as ppl
import matplotlib.pyplot as plt
import numpy as np

np.random.seed(12)

fig, ax = plt.subplots(1)

ppl.hist(ax, np.random.randn(100), grid='y')
ax.set_yscale('log')
ax.set_ylim(0, 25)

plt.show()

When I try to install, I get the following error message:

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

This seems to be problem with the recently updated xcode. A temporary solution is given here (http://kaspermunck.github.io/2014/03/fixing-clang-error/). Would it be possible to implement it into prettypot?

• Guidelines from numpy: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
• [numpydoc](https://pypi.python.org/pypi/numpydoc) for creating sphinx-generated documentation

Is there a way to change the default color set from ColorBrewer set 2 to something else (e.g. ColorBrewer set 1)?

The first three figures on the front page are linked incorrectly. Probably they should go to Examples-with-code instead of Examples-gallery.

Suggest adding for so that lines 403-405 become:

if grid is not None:
    for g in grid:
        assert g in ('x', 'y')
        ax.grid(axis=g, color='white', linestyle='-', linewidth=0.5)

When I use the pcolormesh function many times inside suplots, all the color bars appear until the end of the plot. See figure

Thanks

Hi @olgabot. Do you plan on uploading a new release on PyPI soon? I would like to have "pip install prettyplotlib" fetch the code with the Python 3 compatibility changes, instead of having to point pip to the GitHub repo.

Compare

import matplotlib.pyplot as plt, prettyplotlib as ppl
f, (ax1, ax2) = plt.subplots(2)
f.subplots_adjust(hspace=0)
plt.show()

and

import matplotlib.pyplot as plt, prettyplotlib as ppl
f, (ax1, ax2) = plt.subplots(2)
f.subplots_adjust(hspace=0)
ppl.plot(ax1, [1], [1])
ppl.plot(ax2, [1], [1])
plt.show()

In the second case, by drawing white axes (I guess) around the lower plot, the upper plot's x-axis gets erased.

In #13, @ilblackdragon mentioned that pip can sometimes fetch the wrong distribution file of prettyplotlib. More specifically

• pip seems to be attempting to fetch the OS X 10.9 tarball for platforms that are not OS X.
• using pip inside a virtualenv does not seem to suffer from this problem

@ilblackdragon, is there a chance that the pip versions are different for your system-wide installation than the ones inside your virtualenvs?

@olgabot Is there a reason for a tarball built specifically for OS X 10.9? prettyplotlib has no extension modules that need to be built for any specific platform and is a pure Python package. I see that it's meant to be untarred at the root directory so that it unpacks into /usr/local/lib/python2.7/site-packages/prettyplotlib, but this isn't even the right directory to unpack to for most OS X users since OS X uses the whole "Framework Python" layout (unless the user has explicitly installed a non-Framework Python via MacPorts or Homebrew). I'm not sure this extra tarball is helpful and it seems detrimental in the case of confusing pip on which tarball it should fetch.

When I try to run your scatter plot example (https://github.com/olgabot/prettyplotlib/wiki/Examples-with-code#scatter-points), I can only see green colors in all the points. I am not ablle to see all the different colors in the plot.

The bar plots annotate all float data with 3 digits of precision. Is it possible to control this? Maybe have a new user defined parameter that can be used to set the precision of the data in case of floats.

Need to supply color=color so that it fills, otherwise get an empty rectangle. This is a bug related to matplotlib filling patches by default, which was turned off in the rcParams:

# Default empty circle with a colored outline
mpl.rcParams['patch.facecolor'] = 'none'
mpl.rcParams['patch.edgecolor'] = set2[0]

The package description on PyPI doesn't look very nice (many escape sequences and some useless HTML code). Is there a way to get a cleaner description up there?

fig1=plt.figure()
ax1=fig1.gca()
im1=ax1.imshow(tab_amp,cmap=cm.rainbow,extent=(0,90,-45,45),interpolation='bilinear')
ax1.set_xlabel(u'\u03b8 (°)')
ax1.set_ylabel(u'\u03c6 (°)')
cb1=fig1.colorbar(im1)
cb1.set_label(u'Amplitude de \u03b8ij (°)')
cs1 = ax1.contour(tab_amp_inv,colors='k',extent=(0,90,-45,45))
ax1.clabel(cs1, inline=1, fontsize=10,color='k')

I worked before then I installed prettyplotlib and now I gives this

I think prettyplotlib has changed the default font in python to a font that doesn't allow unicode character. How can I changed it back?

Hi,
When I try to run
colors = {nucleotide: ppl.set2[i] for i, nucleotide in enumerate(nucleotides)}
As shown in:
https://github.com/olgabot/prettyplotlib/wiki/Examples-with-code#bar-correctly-annotates-negative-values

I get an error:
AttributeError: 'module' object has no attribute 'set2'

I am not sure but I looked at the code and I think you are not importing it (since only bits of colors.py are imported and not the whole module).

Suggested by Phillip Guo so the objects can be further modified.

pydoc prettyplotlib.general doesn't show any results because it thinks the subplots and subplot2grid functions are defined in the pyplot module, as functools.wraps has modified their __module__ attribute. Instead, I think only the __doc__ and __wrapped__ attributes should be set, either manually or using functools.update_wrapper (setting __wrapped__ properly also sets the correct signature in pydoc).

The vert keyword argument in matplotlib makes the boxes horizontal when set to false. This isn't handled well by prettyplotlib as all of the labels and the spline retain their original positions.

When using prettyplotlib you have to think before every function call whether it is a plotting command implemented in prettyplotlib or some other command solely implemented in pyplot (of matplotlib). These cognitive resources could be spared if it was possible to completely switch over to prettyplotlib for all functions.

To give an example, it would be nice instead of writing

import matplotlib.pyplot as plt
import prettyplotlib as ppl

# produce data to plot

ppl.plot(x, y)
plt.xlabel('$x$')
plt.ylabel('$y$')

to be able to write

ppl.plot(x, y)
ppl.xlabel('$x$')
ppl.ylabel('$y$')

Are any other people considering this a worthwhile feature?

For implementing this I see two possibilities:

1. For each pyplot function implement one function in prettyplotlib calling the pyplot function. This could be quite some work and might break when the pyplot API changes.
2. Use this “hack” to dynamically map calls to functions not defined in prettyplotlib to pyplot. I am not completely sure what problems could occur with this approach. I think, it might prevent code completion in some editors or syntax checking might be less accurate.

when having more than about 25 lables on the x-axis (say 50) is not handled properly(overlapping lables) or is there a command to fix it ?