Re: [Matplotlib-users] linearized log axis

[Eric F. <ef...@ha...>]

On 05/19/2010 11:31 PM, Christer Malmberg wrote:
> Thank you for the help, I never knew what the symlog flag did actually.
>
> However, there is still a slight problem:
>
> =====================================================
> x = array([0,1,2,4,6,9,12,24])
> y = array([1000000, 500000, 100000, 100, 5, 1, 1, 1])
> subplot(111)
> plot(x, y)
> yscale('symlog')
> xscale=('linear')
> ylim(-1,10000000)
> show()
> =====================================================
>
> The plot looks exactly like I want it, the problem is when I change the
> "1"'s to "0"'s in the y-array, then I get a:
>
> File "C:\Python26\lib\site-packages\matplotlib\ticker.py", line 1029, in
> is_decade
> lx = math.log(x)/math.log(base)
> ValueError: math domain error
>
> I suppose that means somewhere a log(0) is attempted. This kind of
> defeats the purpose...

Yes, it looks like a bug that can be fixed fairly easily.  In the 
meantime, a workaround is to add the kwarg "scaley=False" to your call 
to "plot"; or more generally, do something like

ax = subplot(111)
ax.set_autoscaley_on(False)

before proceeding with any plotting commands.

Eric


>
> /C
>
> Quoting Eric Firing <ef...@ha...>:
>
>> On 05/19/2010 10:28 AM, Benjamin Root wrote:
>>> Maybe I am misunderstanding your problem, but you can select 'semilog'
>>> for the x/yscale parameter.
>>
>> You mean "symlog".
>>
>> See
>> http://matplotlib.sourceforge.net/examples/pylab_examples/symlog_demo.html
>>
>>
>> Although the example doesn't show it, the axis limits don't have to be
>> symmetric. For example, on the top plot, you can use
>>
>> gca().set_xlim([0, 100])
>>
>> to show only the right-hand side.
>>
>> Eric
>>
>>
>>>
>>> Ben Root
>>>
>>> On Wed, May 19, 2010 at 7:03 AM, Christer Malmberg
>>> <Chr...@st...
>>> <mailto:Chr...@st...>> wrote:
>>>
>>> Hi,
>>>
>>> my problem is that I need a graph with a discontinous y-axis. Let me
>>> explain the problem: in my field (microbiology) the data generated
>>> from for example growth assays have a huge range (10^0-10^9), which
>>> has to be plotted on a semilogy style plot (cell concentration vs.
>>> time). The problem is that 0 cells is a useful number to plot
>>> (indicates cell concentration lower than detection limit), but of
>>> course not possible to show in a log diagram. This is easily solved on
>>> old-style logarithmic graph paper; since the data will be either 0, or
>>> >1 it is customary just to draw a zero x-axis at 10^-1 on the paper
>>> and that's that. On the computer, this is extremely hard. Most people
>>> I know resort to various tricks in Excel, such as entering a small
>>> number (0.001 etc) and starting the y-axis range from 10^1 to hide the
>>> problem. This makes excel draw a line, instead of leaving out the dot
>>> and line entirely. The part of the curve below the x-axis is then
>>> manually cut off in a suitable image editor. Needless to say, this is
>>> extremely kludgy. Even professional graphing packages like Graphpad
>>> Prism resort to similar kludges (re-define 0 values to 0.1, change the
>>> y-axis tick label to "0" etc.) This problem of course exists in other
>>> fields, while investigating a solution I found a guy who worked with
>>> aerosol contamination in clean rooms, and he needed to plot values
>>> logarithmically, at the same time as showing detector noise around
>>> 1-10 particles. He solved it by the same trick I would like to do in
>>> Matplotlib, namely plotting a standard semilogy plot but with the
>>> 10^-1 to 10^0 decade being replaced by a 0-1 linear axis on the same
>>> side.
>>>
>>> The guy in this post has the same problem and a useful example:
>>> http://ubuntuforums.org/showthread.php?t=394851
>>>
>>> His partial solution is quite bad though, and I just got stuck while
>>> trying to improve it. I looked around the gallery for useful examples,
>>> and the closest I could find is the twinx/twiny function, but I didn't
>>> manage a plot that put one data curve across both axes.
>>>
>>> This code gives an image that maybe explains what I'm trying to do:
>>>
>>> =======================================
>>> t = array([0,1,2,4,6,9,12,24])
>>> y = array([1000000, 500000, 100000, 100, 5, 1, 0, 0])
>>> subplot(111, xscale="linear", yscale="log")
>>> errorbar(x, y, yerr=0.4*y)
>>> linbit = axes([0.125, 0.1, 0.775, 0.1],frameon=False)
>>> linbit.xaxis.set_visible(False)
>>> for tl in linbit.get_yticklabels():
>>> tl.set_color('r')
>>> show()
>>> =======================================
>>>
>>> (the y=0 points should be plotted and connected to the line in the
>>> log part)
>>>
>>> Is this possible to do in matplotlib? Could someone give me a pointer
>>> on how to go on?
>>>
>>> Sorry for the long mail,
>>>
>>> /C
>>>
>>>
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