Matplotlib: avoiding overlapping datapoints in a "scatter/dot/beeswarm" plot

Question

When drawing a dot plot using matplotlib, I would like to offset overlapping datapoints to keep them all visible. For example, if I have:

CategoryA: 0,0,3,0,5   CategoryB: 5,10,5,5,10   

I want each of the CategoryA "0" datapoints to be set side by side, rather than right on top of each other, while still remaining distinct from CategoryB.

In R (ggplot2) there is a "jitter" option that does this. Is there a similar option in matplotlib, or is there another approach that would lead to a similar result?

Edit: to clarify, the "beeswarm" plot in R is essentially what I have in mind, and pybeeswarm is an early but useful start at a matplotlib/Python version.

Edit: to add that Seaborn's Swarmplot, introduced in version 0.7, is an excellent implementation of what I wanted.

Answer 1

Extending the answer by @user2467675, here’s how I did it:

def rand_jitter(arr):     stdev = .01 * (max(arr) - min(arr))     return arr + np.random.randn(len(arr)) * stdev  def jitter(x, y, s=20, c='b', marker='o', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, verts=None, hold=None, **kwargs):     return scatter(rand_jitter(x), rand_jitter(y), s=s, c=c, marker=marker, cmap=cmap, norm=norm, vmin=vmin, vmax=vmax, alpha=alpha, linewidths=linewidths, **kwargs) 

The stdev variable makes sure that the jitter is enough to be seen on different scales, but it assumes that the limits of the axes are zero and the max value.

You can then call jitter instead of scatter.