matplotlib-users Mailing List for matplotlib

Benjamin Root wrote:

> On Sunday, September 25, 2011, Andreas Matthias <and...@gm...>
> wrote:
>> Paul Ivanov wrote:
>> 
>>> On Sat, Sep 24, 2011 at 3:59 AM, Andreas Matthias
>>> <and...@gm...> wrote:
>>>> Hmm. I do not get a reversed list of axes. This is the output of
>>>> the example code below:
>>>> 
>>>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>,
> <matplotlib.axes.Axes object at 0x8f633ec>]
>>>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>,
> <matplotlib.axes.Axes object at 0x8f633ec>]
>>> 
>>> This doesn't seem right - for me that code results in:
>>> [<matplotlib.axes.AxesSubplot object at 0x16d7de70>,
>>> <matplotlib.axes.Axes object at 0x1b77c890>]
>>> [<matplotlib.axes.Axes object at 0x1b77c890>,
>>> <matplotlib.axes.AxesSubplot object at 0x16d7de70>]
>>> 
>>> can you try explicitly swapping your axes? f.axes =
>>> [f.axes[1],f.axes[0]] instead of the call to reverse?
>> 
>> Traceback (most recent call last):
>>  File "t5.py", line 13, in <module>
>>    f.axes = [f.axes[1],f.axes[0]]
>> AttributeError: can't set attribute
>> 
>> 
>> I've tried it with matplotlib 1.0.1 and 1.1.0. Same error message.
>> Python is 2.6.4.
>> I'm stumped ...
> 
> Sometimes installations can get mixed up.  What does:
> 
> Import matplotlib
> print matplotlib.__version__
> print matplotlib.__file__
> 
> outputs for your v1.1.0 installation and your v1.0.1 install?

1.1.0
/home/andreas/local/python/lib/python2.6/site-packages/matplotlib/__init__.pyc

This is the right place. Then I removed matplotlib/ and
installed it again. But the error stays the same.

Ciao
Andreas

On Sunday, September 25, 2011, Andreas Matthias <and...@gm...>
wrote:
> Paul Ivanov wrote:
>
>> On Sat, Sep 24, 2011 at 3:59 AM, Andreas Matthias
>> <and...@gm...> wrote:
>>> Hmm. I do not get a reversed list of axes. This is the output of
>>> the example code below:
>>>
>>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>,
<matplotlib.axes.Axes object at 0x8f633ec>]
>>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>,
<matplotlib.axes.Axes object at 0x8f633ec>]
>>
>> This doesn't seem right - for me that code results in:
>> [<matplotlib.axes.AxesSubplot object at 0x16d7de70>,
>> <matplotlib.axes.Axes object at 0x1b77c890>]
>> [<matplotlib.axes.Axes object at 0x1b77c890>,
>> <matplotlib.axes.AxesSubplot object at 0x16d7de70>]
>>
>> can you try explicitly swapping your axes? f.axes =
>> [f.axes[1],f.axes[0]] instead of the call to reverse?
>
> Traceback (most recent call last):
>  File "t5.py", line 13, in <module>
>    f.axes = [f.axes[1],f.axes[0]]
> AttributeError: can't set attribute
>
>
> I've tried it with matplotlib 1.0.1 and 1.1.0. Same error message.
> Python is 2.6.4.
> I'm stumped ...
>
>
> Ciao
> Andreas
>

Sometimes installations can get mixed up.  What does:

Import matplotlib
print matplotlib.__version__
print matplotlib.__file__

outputs for your v1.1.0 installation and your v1.0.1 install?

Ben Root

Paul Ivanov wrote:

> On Sat, Sep 24, 2011 at 3:59 AM, Andreas Matthias
> <and...@gm...> wrote:
>> Hmm. I do not get a reversed list of axes. This is the output of
>> the example code below:
>> 
>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>, <matplotlib.axes.Axes object at 0x8f633ec>]
>> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>, <matplotlib.axes.Axes object at 0x8f633ec>]
> 
> This doesn't seem right - for me that code results in:
> [<matplotlib.axes.AxesSubplot object at 0x16d7de70>,
> <matplotlib.axes.Axes object at 0x1b77c890>]
> [<matplotlib.axes.Axes object at 0x1b77c890>,
> <matplotlib.axes.AxesSubplot object at 0x16d7de70>]
> 
> can you try explicitly swapping your axes? f.axes =
> [f.axes[1],f.axes[0]] instead of the call to reverse?

Traceback (most recent call last):
  File "t5.py", line 13, in <module>
    f.axes = [f.axes[1],f.axes[0]]
AttributeError: can't set attribute


I've tried it with matplotlib 1.0.1 and 1.1.0. Same error message.
Python is 2.6.4.
I'm stumped ...


Ciao
Andreas

Dear all,

Heatmap (like those on the page 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/) 
is a frequently used type of image in microarray data analysis. However, 
it seems there are no convenient functions in matplotlib to plot heatmap 
(please correct me if I was wrong), so I'm planning to write my own.

Let me take the heatmap by the link 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/scaled_color_key.png 
as an example, which is produced by R.

With my limited knowledge and expertise of matplotlib, I have the 
following questions and I hope you guys could help me.

1) I tend to use pcolor to draw the colormap in the central area. 
However, I've seen a lot of examples draw colormap with imshow.

     What's the difference between pcolor and imshow?
     Shall I use pcolor or imshow to produce the heatmap in the link above?

2) How to draw the dendrograms on the top and left of the colormap?

     I got hints from 
http://matplotlib.sourceforge.net/examples/axes_grid/scatter_hist.html 
on how to append axes to current plot, but I still have now idea how to 
draw the dengrograms.

3) How to draw the column side colormap (the smaller one) between the 
top dendrogram and the big colormap?

4) I can use colorbar to draw a colorbar, but how to place the colorbar 
on the topleft of the image just as the R heatmap does?

5) Any other suggestions on how to draw the heatmap?

Thanks and any help will be greatly appreciated.

Regards,
Jianfeng

  Dear all,

Heatmap (like those on the page 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/) 
is a frequently used type of image in microarray data analysis. However, 
it seems there are no convenient functions in matplotlib to plot heatmap 
(please correct me if I was wrong), so I'm planning to write my own.

Let me take the heatmap by the link 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/scaled_color_key.png 
as an example, which is produced by R.

With my limited knowledge and expertise of matplotlib, I have the 
following questions and I hope you guys could help me.

1) I tend to use pcolor to draw the colormap in the central area. 
However, I've seen a lot of examples draw colormap with imshow.

    What's the difference between pcolor and imshow?
    Shall I use pcolor or imshow to produce the heatmap in the link above?

2) How to draw the dendrograms on the top and left of the colormap?

    I got hints from 
http://matplotlib.sourceforge.net/examples/axes_grid/scatter_hist.html 
on how to append axes to current plot, but I still have now idea how to 
draw the dengrograms.

3) How to draw the column side colormap (the smaller one) between the 
top dendrogram and the big colormap?

4) I can use colorbar to draw a colorbar, but how to place the colorbar 
on the topleft of the image just as the R heatmap does?

5) Any other suggestions on how to draw the heatmap?

Thanks and any help will be greatly appreciated.

Regards,
Jianfeng

On Sat, Sep 24, 2011 at 3:59 AM, Andreas Matthias
<and...@gm...> wrote:
> Hmm. I do not get a reversed list of axes. This is the output of
> the example code below:
>
> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>, <matplotlib.axes.Axes object at 0x8f633ec>]
> [<matplotlib.axes.AxesSubplot object at 0x8d8fb4c>, <matplotlib.axes.Axes object at 0x8f633ec>]

This doesn't seem right - for me that code results in:
[<matplotlib.axes.AxesSubplot object at 0x16d7de70>,
<matplotlib.axes.Axes object at 0x1b77c890>]
[<matplotlib.axes.Axes object at 0x1b77c890>,
<matplotlib.axes.AxesSubplot object at 0x16d7de70>]

can you try explicitly swapping your axes? f.axes =
[f.axes[1],f.axes[0]] instead of the call to reverse?

> BTW, what's matplotlib.axes.AxesSubplot? I couldn't find this class.

see  SubplotBase class and subplot_class_factory function in matplotlib/axes.py

best,
--
Paul Ivanov
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