linearized log axis

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])
plot(x, y)

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\", line 1029, in
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)

before proceeding with any plotting commands.



On 05/19/2010 11:31 PM, Christer Malmberg wrote:


Quoting Eric Firing <efiring@...202...>:

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".


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.


Ben Root

On Wed, May 19, 2010 at 7:03 AM, Christer Malmberg >>> <Christer.Malmberg.0653@...3109... >>> <mailto:Christer.Malmberg.0653@…3109…>> wrote:


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

The guy in this post has the same problem and a useful example:
plotting with mixed logarithmic/linear scales

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)
for tl in linbit.get_yticklabels():

(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,



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