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 errorI 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

## ···

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

/C

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".

See

http://matplotlib.sourceforge.net/examples/pylab_examples/symlog_demo.htmlAlthough the example doesn't show it, the axis limits don't have to be

symmetric. For example, on the top plot, you can usegca().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.0653@...3109... >>> <mailto:Christer.Malmberg.0653@…3109…>> 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:

plotting with mixed logarithmic/linear scalesHis 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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