matplotlib-users Mailing List for matplotlib

Hi all,
I have what seems to be a small error trying to reference a function in the
compiled tk backend which doesn't exist in the shared object (See stack
trace below). I'm running on a 64-bit system.
Has anyone else had this issue? Google didn't reveal a lot to me (searching
for "undefined symbol: XCreateIC" exact phrase yielded 2 results, neither
very enlightening for me.
python -c `import matplotlib; print matplotlib.__version__`:
0.99.3
To repeat this error (for me), simply run
python -c 'import pylab'
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/pylab.py", line 1,
in <module>
 from matplotlib.pylab import *
 File
"/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/pylab.py",
line 247, in <module>
 from matplotlib.pyplot import *
 File
"/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/pyplot.py",
line 78, in <module>
 new_figure_manager, draw_if_interactive, show = pylab_setup()
 File
"/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/backends/__init__.py",
line 25, in pylab_setup
 globals(),locals(),[backend_name])
 File
"/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py",
line 8, in <module>
 import tkagg # Paint image to Tk photo blitter extension
 File
"/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/backends/tkagg.py",
line 1, in <module>
 import _tkagg
ImportError:
/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/backends/_tkagg.so:
undefined symbol: XCreateIC
>>> import tkagg
Output from --verbose:
CONFIGDIR=/home/ho/nmc/tjl/.matplotlib
matplotlib data path
/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/mpl-data
loaded rc file
/home/ho/nmc/tjl/nltk/lib/python2.6/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 0.99.3
verbose.level helpful
interactive is False
units is False
platform is linux2
Using fontManager instance from /home/ho/nmc/tjl/.matplotlib/fontList.cache
-- 
--------------------------------------------------
Tennessee Leeuwenburg
http://myownhat.blogspot.com/
"Don't believe everything you think"

On 06/05/2010 04:41 PM, per freem wrote:
> Hi all,
>
> How can I plot a matrix of values as a heatmap where values are shown
> from green to red intensities, or blue to yellow intensities, like in
> the following figure?
>
> http://www.coriell.org/images/microarray.gif
>
> I want to have the option of doing this with either green-red maps or
> blue-yellow maps. Is the right function for this imshow, or pcolor?
pcolor is general but slow, and best suited for moderate numbers of 
points. pcolormesh is faster. imshow can be good if you have a uniform 
Cartesian grid. imshow(...., interpolation='nearest') is the closest 
analogy to pcolor and pcolormesh.
> Also, how can I get the scale bar to the left of it that shows the
> ranges of the intensities, and how can this scale be adjusted?
In the gallery, and in the corresponding examples subdirectory of the 
mpl distribution, search for "colorbar". Note that the color scale is 
not set via colorbar options, but via vmin and vmax kwargs in imshow 
etc., or via the pylab clim command, or via the set_clim method of the 
image object returned by imshow. In other words, the colorbar is used 
for showing a color scale used by another image-like plot element--it is 
not used for controlling that scale, or any other aspect of the image 
itself.
Eric
>
> Thanks very much.
>
> ------------------------------------------------------------------------------
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I think what you are looking for is a way to specify the colormap of your
plot. While the documentation is a little sparse on this topic, there is
plenty of functionality in matplotlib regarding colormaps.
Here is a list of built-in colormaps:
http://matplotlib.sourceforge.net/api/pyplot_api.html?highlight=colormap#matplotlib.pyplot.colormaps
Just about any matplotlib plotting function accepts a cmap keyword where you
can specify a colormap of your choice to override the default. You can even
create your own colormap if you can't find one to suit your needs.
I hope this is helpful.
Ben Root
On Sat, Jun 5, 2010 at 9:41 PM, per freem <per...@gm...> wrote:
> Hi all,
>
> How can I plot a matrix of values as a heatmap where values are shown
> from green to red intensities, or blue to yellow intensities, like in
> the following figure?
>
> http://www.coriell.org/images/microarray.gif
>
> I want to have the option of doing this with either green-red maps or
> blue-yellow maps. Is the right function for this imshow, or pcolor?
> Also, how can I get the scale bar to the left of it that shows the
> ranges of the intensities, and how can this scale be adjusted?
>
> Thanks very much.
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit. See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

--- On Sun, 6/6/10, Brice Thurin <br...@4d...> wrote:
> I was wondering if someone could let know what is the
> status of the two backends and if the CocoaAgg backend is
> still supported as it does not appear in the list of backend
> in the Faq.
As far as I can tell it still works, but it doesn't seem to be up to date with the other backends.
> I saw in one of the post of Michiel de Hoon dating back
> 2008 that the MacOsX backend does not allow for integration
> of matplotlib within a cocoa application, I was wondering if
> it is still the case.
Maybe "does not allow" is too strong an expression. The MacOSX backend was not designed to be integrated within a cocoa application, but somebody sufficiently familiar with cocoa may be able to find a way to do so.
> Also, I tried to find some tutorial or example showing how
> to use the two backend but could not find one, maybe i
> overlooked something and would be grateful if someone could
> point it to me.
> 
What do you mean by how to use the backend? In principle, the MacOSX backend has the same functionality as the other GUI backends.
--Michiel.
 

Good Morning,
I was wondering if someone could let know what is the status of the two backends and if the CocoaAgg backend is still supported as it does not appear in the list of backend in the Faq.
I saw in one of the post of Michiel de Hoon dating back 2008 that the MacOsX backend does not allow for integration of matplotlib within a cocoa application, I was wondering if it is still the case.
Also, I tried to find some tutorial or example showing how to use the two backend but could not find one, maybe i overlooked something and would be grateful if someone could point it to me.
I thank you in advance for any response and for this great package.
Regards,
Brice

Hi all,
How can I plot a matrix of values as a heatmap where values are shown
from green to red intensities, or blue to yellow intensities, like in
the following figure?
http://www.coriell.org/images/microarray.gif
I want to have the option of doing this with either green-red maps or
blue-yellow maps. Is the right function for this imshow, or pcolor?
Also, how can I get the scale bar to the left of it that shows the
ranges of the intensities, and how can this scale be adjusted?
Thanks very much.