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If I rotate the xticks labels on this scatter plot the axes label is pushed off the figure. Do I
need to make the figuresize bigger or is matplotlib calculating it incorrectly?



from pylab import *

prediction_experiment = [(0.0001, 0.0001),(2, 250.797999999999998), (313.11000000000001,
25.797999999999998), (4499.1999999999998, 25000.0), (168830.0, 440000.0), (143090.0,
78571.399999999994), (34811.0, 78571.399999999994), (161240.0, 70967.699999999997)]

def roundUpLogDecade(x):
    """ Round up to the nearest logarithmic decade"""
    return math.ceil(x)

def roundDownLogDecade(x):
    """ Round up to the nearest logarithmic decade"""
    return math.floor(x)

def integer(x, pos):
    if x >= 1:
       return '%i' % (int(x))
    else:
        return '%.4f' % x

auc_cutoff = 50

ax = subplot(111)
# Axis scale must be set prior to declaring the Formatter
# If it is not the Formatter will use the default log labels for ticks.
ax.set_xscale('log')
ax.set_yscale('log')

formatter = FuncFormatter(integer)
ax.xaxis.set_major_formatter(formatter)
ax.yaxis.set_major_formatter(formatter)

tp_prediction_experiment = [[x[0], x[1]] for x in prediction_experiment if x[1] < auc_cutoff]
tn_prediction_experiment = [[x[0], x[1]] for x in prediction_experiment if x[1] > auc_cutoff]

ax.scatter( [x[0] for x in tn_prediction_experiment], [x[1] for x in tn_prediction_experiment],
s=3, c='r', marker='s', faceted=False)
ax.scatter( [x[0] for x in tp_prediction_experiment], [x[1] for x in tp_prediction_experiment],
s=3, c='b', marker='s', faceted=False)

# Must add 1 to allow the last decades label to be shown
ax.set_xlim(10**roundDownLogDecade(log10(min([x[0] for x in prediction_experiment]))),
10**roundUpLogDecade(log10(max([x[0] for x in prediction_experiment])))+1)
ax.set_ylim(10**roundDownLogDecade(log10(min([x[1] for x in prediction_experiment]))),
10**roundUpLogDecade(log10(max([x[1] for x in prediction_experiment])))+1)
grid(True)        
xlabel(r"Prediction", fontsize = 12)
ylabel(r"Experimental IC50 [nM]", fontsize = 12)

xlocs, xlabels = xticks()
setp(xlabels, rotation=45)
ylocs, ylabels = yticks()
setp(ylabels, rotation=45)

show()

Thanks,
Derek Basch

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Michael,

Thanks, this is now fixed in svn.

Eric

O'Keefe, Michael wrote:
> Line 733 in ticker.py in matplotlib 0.87.2 has a potential divide by zero error:
> 
> var = dv/max(abs(vmin),abs(vmax))
> 
> I've triggered it with the following:
> 
> import pylab
> import numpy as np
> t = np.array([0.,1.,2.,3.],float)
> a = np.array([0.,0.,0.,0.],float)
> pylab.plot(t,a)
> 
> The error is:
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "C:\Python24\Lib\site-packages\matplotlib\pylab.py", line 2018, in plot
>     ret =  gca().plot(*args, **kwargs)
>   File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 2790, in plot
>     self.autoscale_view()
>   File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 817, in autoscal
> e_view
>     self.set_ylim(locator.autoscale())
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 798, in autosc
> ale
>     return take(self.bin_boundaries(dmin, dmax), [0,-1])
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 768, in bin_bo
> undaries
>     scale, offset = scale_range(vmin, vmax, nbins)
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 733, in scale_
> range
>     var = dv/max(abs(vmin), abs(vmax))
> ZeroDivisionError: float division
> 
> 
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I'm using 0.86.2 (Debian 0.86.2-3).  With the following line in
matplotlibrc, 

    font.sans-serif     : Courier 10 Pitch, Bitstream Vera Sans, Lucida Grande, Verdana, Geneva, Lucida, Bitstream Vera Sans, Arial, Helvetica, sans-serif

when I run 
    
    python embedding_in_wx.py
    python embedding_in_wx2.py
    python embedding_in_wx3.py
    python embedding_in_gtk.py

I see the Courier font used.  But when I run

    python embedding_in_gtk3.py
    python embedding_in_qt.py
    python embedding_in_tk.py
    python embedding_in_tk2.py
    python embedding_in_wx4.py

I see the Lucida Grande font used.  Any ideas?

Thank you,
Glen Mabey

You may double check to see that MPL is finding the correct versions  
of Freetype.  There is a version in Apple's X11 that does not work  
with MPL -- make sure you are not picking up this one by mistake.   
Otherwise, the build method you described has worked for me.  It  
seems like you are doing all the right things.

-Rob.



On Mar 22, 2006, at 12:17 PM, Tom Loredo wrote:

>
> Hi folks,
>
> I've just installed MacPy 2.4.1, the latest numpy & scipy, and
> mpl-0.87.2 on a colleague's Panther PowerBook.  numpy & scipy
> installed fine and passed all tests.  For mpl, we installed
> zlib from source, and initially installed Freetype2 and libpng
> via the i-Installer.  mpl built and installed fine, but gave
> a bus error when trying to plot ("import matplotlib" would
> work fine, but "import pylab" would give the error).
>
> The .matplotlib/matplotlibrc file we're using does have TkAgg
> and numpy specified, and we've verified that Tkinter is
> working via a "Hello World" test script.
>
> Suspecting one of the libraries, we then installed Freetype2
> and libpng from source.  We deleted all the mpl stuff in
> site-packages and the mpl build directory, and built and
> installed mpl again from scratch.  We still get a bus error
> from pylab.  I am stumped as to what to try next.  I've
> copied verbose output below; I hope someone can offer us
> some clues.
>
> Thanks,
> Tom Loredo
>
> $ pythonw simple_plot.py --verbose-debug-annoying
> matplotlib data path
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ 
> site-packages/matplotlib/mpl-data
> $HOME=/Users/bill
> CONFIGDIR=/Users/bill/.matplotlib
> loaded rc file /Users/bill/.matplotlib/matplotlibrc
> matplotlib version 0.87.2
> verbose.level debug-annoying
> interactive is False
> platform is darwin
> loaded modules: ['pylab', '_bisect', '__future__', 'copy_reg',
> 'sre_compile', 'distutils', 'itertools', '_sre', '__main__', 'site',
> '__builtin__', 'datetime', 'matplotlib.re', 'matplotlib.tempfile',
> 'encodings', 'pytz.datetime', 'shutil', 'distutils.string',
> 'dateutil', 'matplotlib.datetime', 'posixpath', '_random',
> 'tempfile', 'errno', 'matplotlib.warnings', 'binascii',
> 'encodings.codecs', 'sre_constants', 're', 'matplotlib.md5',
> 'os.path', 'pytz.sys', '_codecs', 'distutils.sysconfig',
> 'encodings.exceptions', 'pytz.sets', 'math', 'fcntl', 'stat',
> 'zipimport', 'string', 'warnings', 'encodings.types', 'UserDict',
> 'encodings.ascii', 'matplotlib.sys', 'matplotlib', 'distutils.os',
> 'sys', 'pytz.tzinfo', 'pytz', 'matplotlib.__future__', 'codecs',
> 'distutils.re', 'matplotlib.pytz', 'types', 'md5',
> 'matplotlib.dateutil', 'matplotlib.os', 'thread', 'sre', 'bisect',
> 'matplotlib.distutils', 'signal', 'distutils.errors', 'random',
> 'linecache', 'matplotlib.shutil', 'posix', 'encodings.aliases',
> 'sets', 'exceptions', 'sre_parse', 'pytz.bisect', 'distutils.sys',
> 'os', 'strop']
> numerix numpy 0.9.6
> Bus error
>
>
>
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-----
Rob Hetland, Assistant Professor
Dept of Oceanography, Texas A&M University
p: 979-458-0096, f: 979-845-6331
e: he...@ta..., w: http://pong.tamu.edu

This came up on the dev list, and I believe is fixed in svn now.

Thanks,

On 3/23/06, O'Keefe, Michael <Mic...@nr...> wrote:
> Line 733 in ticker.py in matplotlib 0.87.2 has a potential divide by zero=
 error:
>
> var =3D dv/max(abs(vmin),abs(vmax))
>
> I've triggered it with the following:
>
> import pylab
> import numpy as np
> t =3D np.array([0.,1.,2.,3.],float)
> a =3D np.array([0.,0.,0.,0.],float)
> pylab.plot(t,a)
>
> The error is:
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "C:\Python24\Lib\site-packages\matplotlib\pylab.py", line 2018, in=
 plot
>     ret =3D  gca().plot(*args, **kwargs)
>   File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 2790, in =
plot
>     self.autoscale_view()
>   File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 817, in a=
utoscal
> e_view
>     self.set_ylim(locator.autoscale())
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 798, in=
 autosc
> ale
>     return take(self.bin_boundaries(dmin, dmax), [0,-1])
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 768, in=
 bin_bo
> undaries
>     scale, offset =3D scale_range(vmin, vmax, nbins)
>   File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 733, in=
 scale_
> range
>     var =3D dv/max(abs(vmin), abs(vmax))
> ZeroDivisionError: float division
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmdlnk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Line 733 in ticker.py in matplotlib 0.87.2 has a potential divide by =
zero error:

var =3D dv/max(abs(vmin),abs(vmax))

I've triggered it with the following:

import pylab
import numpy as np
t =3D np.array([0.,1.,2.,3.],float)
a =3D np.array([0.,0.,0.,0.],float)
pylab.plot(t,a)

The error is:

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "C:\Python24\Lib\site-packages\matplotlib\pylab.py", line 2018, =
in plot
    ret =3D  gca().plot(*args, **kwargs)
  File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 2790, in =
plot
    self.autoscale_view()
  File "C:\Python24\Lib\site-packages\matplotlib\axes.py", line 817, in =
autoscal
e_view
    self.set_ylim(locator.autoscale())
  File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 798, =
in autosc
ale
    return take(self.bin_boundaries(dmin, dmax), [0,-1])
  File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 768, =
in bin_bo
undaries
    scale, offset =3D scale_range(vmin, vmax, nbins)
  File "c:\python24\lib\site-packages\matplotlib\ticker.py", line 733, =
in scale_
range
    var =3D dv/max(abs(vmin), abs(vmax))
ZeroDivisionError: float division

On 3/22/06, lan...@qw... <lan...@qw...> wrote:
> Does matplotlib work with AquaTerm as a backend?

Recently an AquaTerm backend was donated to matplotlib.  I haven't had
a chance to test or commit it to svn yet though.  I am attaching it
for anyone interested.

- Charlie

Hi John,

I've found the source of this figimage problem.
In _backend_agg.cpp RendererAgg::draw_image is expecting 4 arguments and 
is being passed 5 by the FigureImage draw method in image.py
The offending line is:

renderer.draw_image(self.ox, self.oy, im, self.origin, self.figure.bbox)

Changing this to

renderer.draw_image(self.ox, self.oy, im, self.figure.bbox)

solved the problem for me.

I checked and found that the RendererAgg draw_image() virtual method has 
5 arguments, which seems to be the source of the problem, so either this 
needs changing or the backend code does.

_draw_image() in backend_agg.py makes the call with 3 arguments, so this 
needs fixing too.

The draw_image() method in backend_emf.py has a stub override with 5 
arguments, so this may need changing too, although it isn't causing harm 
yet. I'm not sure all of these are real problems because I didn't try 
too hard to understand how the backends work.

regards,
Gary R.

John Hunter wrote:
>>>>>> "gruben@bigpond" == gruben@bigpond net au <gr...@bi...> writes:
> 
>     gruben@bigpond> It's possible I've done something stupid, but
>     gruben@bigpond> imshow works, so I don't think so. I suspect this
>     gruben@bigpond> may have been broken for a while. I haven't tried
>     gruben@bigpond> 0.87.2 (because I can't be bothered with the new
>     gruben@bigpond> numpy/scipy/matplotlib version interdependency).
> 
> matplotlib does not require numpy or scipy to build or run.  You can
> simply set 'numerix : Numeric' or 'numerix : numarray' in your rc file
> and still use the same old libs you want.  
> 
> So feel free to update to the latest version if you want.  I will look
> into the figimage problem later.
> 
> JDH