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 <efir...@hawaii.edu>: > >> 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 >>> <christer.malmberg.0...@student.uu.se >>> <mailto:christer.malmberg.0...@student.uu.se>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users@lists.sourceforge.net >>> <mailto:Matplotlib-users@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> > > > ------------------------------------------------------------------------------ _______________________________________________ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
