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:
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,