Setting both axes logarithmic in bar plot matploblib

Question

I have already binned data to plot a histogram. For this reason I'm using the plt.bar() function. I'd like to set both axes in the plot to a logarithmic scale.

If I set plt.bar(x, y, width=10, color='b', log=True) which lets me set the y-axis to log but I can't set the x-axis logarithmic. I've tried plt.xscale('log') unfortunately this doesn't work right. The x-axis ticks vanish and the sizes of the bars don't have equal width.

I would be grateful for any help.

Bingaman

Answer 1

By default, the bars of a barplot have a width of 0.8. Therefore they appear larger for smaller x values on a logarithmic scale. If instead of specifying a constant width, one uses the distance between the bin edges and supplies this to the width argument, the bars will have the correct width. One would also need to set the align to "edge" for this to work.

import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)

x = np.logspace(0, 5, num=21)
y = (np.sin(1.e-2*(x[:-1]-20))+3)**10

fig, ax = plt.subplots()
ax.bar(x[:-1], y, width=np.diff(x), log=True,ec="k", align="edge")
ax.set_xscale("log")
plt.show()

I cannot reproduce missing ticklabels for a logarithmic scaling. This may be due to some settings in the code that are not shown in the question or due to the fact that an older matplotlib version is used. The example here works fine with matplotlib 2.0.

Retarder

how would I use this with density=True? – Rivers

This worked for me. One thing I'll add though is the solution gets around a problem by using x[:-1] as the X data, which may not be realistic for actual datasets. To correct this, you can just repeat your last bin width. I created variable to pass to the width argument with: bin_widths = np.pad(np.diff(my_x_data), (0,1), mode="edge") – Wynnie

Answer 2

If the goal is to have equal width bars, assuming datapoints are not equidistant, then the most proper solution is to set width as plt.bar(x, y, width=c*np.array(x), color='b', log=True) for a constant c appropriate for the plot. Alignment can be anything.

Epigenesis

Answer 3

I know it is a very old question and you might have solved it but I've come to this post because I was with something like this but at the y axis and I manage to solve it just using ax.set_ylim(df['my data'].min()+100, df['my data'].max()+100). In y axis I have some sensible information which I thouhg the best way was to show in log scale but when I set log scale I couldn't see the numbers proper (as this post in x axis) so I just leave the idea of use log and use the min and max argment. It sets the scale of my graph much like as log. Still looking for another way for doesnt need use that -+100 at set_ylim.

Goodin

Answer 4

While this does not actually use pyplot.bar, I think this method could be helpful in achieving what the OP is trying to do. I found this to be easier than trying to calibrate the width as a function of the log-scale, though it's more steps. Create a line collection whose width is independent of the chart scale.

import matplotlib.pyplot as plt
import numpy as np
import matplotlib.collections as coll
#Generate data and sort into bins
a = np.random.logseries(0.5, 1000)
hist, bin_edges = np.histogram(a, bins=20, density=False)

x = bin_edges[:-1] # remove the top-end from bin_edges to match dimensions of hist

lines = []
for i in range(len(x)):
    pair=[(x[i],0), (x[i], hist[i])]
    lines.append(pair)

linecoll = coll.LineCollection(lines, linewidths=10, linestyles='solid')
fig, ax = plt.subplots()
ax.add_collection(linecoll)
ax.set_xscale("log")
ax.set_yscale("log")
ax.set_xlim(min(x)/10,max(x)*10)
ax.set_ylim(0.1,1.1*max(hist)) #since this is an unweighted histogram, the logy doesn't make much sense.

Resulting plot - no frills

One drawback is that the "bars" will be centered, but this could be changed by offsetting the x-values by half of the linewidth value ... I think it would be
x_new = x + (linewidth/2)*10**round(np.log10(x),0).

Bandoline