Beeswarm plots in PythonComments
I have recently migrated all of my plots from R to matplotlib. One cool plot type that I was missing from R was the beeswarm. I tried searching for some Python solutions (some discussion on this can be found here and other places online) but was not satisfied with anything I found (if anyone knows of a good implementation out there, I'd be happy to know about it). I made a simple Python implementation of beeswarm, drawing heavily off of the R beeswarm code. This is available as a python package: https://github.com/mgymrek/pybeeswarm. This was whipped up pretty quickly so it is by no means complete. See wishlist at the bottom.
To install, simply do:
git clone https://github.com/mgymrek/pybeeswarm.git
sudo setup.py install
To test that it worked, open up python and check that
import beeswarm doesn't give you any errors.
There is only one function,
from beeswarm import * help(beeswarm)
Help on function beeswarm in module beeswarm.beeswarm: beeswarm(values, positions=None, method='swarm', ax=None, s=20, col='black', xlim=None, ylim=None, labels=None) beeswarm(values, positions=None, method="swarm", ax=None, s=20, col="black", xlim=None, ylim=None, labels=None) Inputs: * values: an array of a sequence of vectors * positions: sets the horizontal positions of the swarms. Ticks and labels are set to match the positions. If none, set positions to range(len(values)) Default: None * method: how to jitter the x coordinates. Choose from "swarm", "hex", "center", "square" Default: swarm * ax: use this axis for plotting. If none supplied, make a new one Default: None * s: size of points in points^2 (assuming 72 points/inch). Defautt: 20 * col: color of points. Can be: - a single string: color all points that color - a vector of strings length len(values): gives color for each group - a vector of strings length sum([len(values[i]) for i in range(len(values))]) gives color for each point - a vector of strings any other length: cycle through the list of colors. (really pretty if not useful) Default: "black" * xlim: tuple giving (xmin, xmax). If not specified, either get from the supplied ax or recalculate * ylim: tuple giving (ymin, ymax). If not specified, eiterh get from the supplied as or recalculate * labels: list of labels for each group. Default: range(len(values)) Returns: * bs: pandas.DataFrame with columns: xorig, yorig, xnew, ynew, color * ax: the axis used for plotting
Here's a small example:
from beeswarm import * import matplotlib.pyplot as plt import numpy as np d1 = np.random.uniform(low=-3, high=3, size=100) d2 = np.random.normal(size=100) bs, ax = beeswarm([d1,d2], method="swarm", labels=["sample 1", "sample 2"], col=["blue","red"])
Here I show what the plots look like for the same examples given on the R beeswarm page for comparison.
Comparing arrangement methods
from beeswarm import beeswarm import matplotlib.pyplot as plt import numpy as np d1 = np.random.uniform(low=-3, high=3, size=100) d2 = np.random.normal(size=100) fig = plt.figure() fig.set_size_inches((8,8)) ax1 = plt.subplot(221) ax2 = plt.subplot(222) ax3 = plt.subplot(223) ax4 = plt.subplot(224) axes = [ax1, ax2, ax3, ax4] methods = ["swarm","center","square","hex"] for i in range(len(axes)): beeswarm([d1, d2], col=["black","red"], method=methods[i], ax=axes[i], labels=["Uniform","Normal"]) axes[i].set_title("Method: %s"%methods[i], size=15) plt.tight_layout()
You can specify one color for everything, one color per group, one color per point, or cycle through colors, given by the four examples below:
fig = plt.figure() fig.set_size_inches((8,8)) ax1 = plt.subplot(221) ax2 = plt.subplot(222) ax3 = plt.subplot(223) ax4 = plt.subplot(224) beeswarm([d1,d2], method="swarm", labels=["Uniform","Normal"], col="black", ax=ax1) beeswarm([d1,d2], method="swarm", labels=["Uniform","Normal"], col=["black","red"], ax=ax2) def GetColor(x): colors =  for item in x: if item > 0: colors.append("red") else: colors.append("blue") return colors colors = GetColor(d1) + GetColor(d2) beeswarm([d1,d2], method="swarm", labels=["Uniform","Normal"], col=colors, ax=ax3) beeswarm([d1,d2], method="swarm", labels=["Uniform","Normal"], col=["red","blue","orange"], ax=ax4) plt.tight_layout()
There are several features that the R package has that I didn't implement here:
- "Corral" methods that keep the data from spreading too far horizontally
- The ability to do horizontal vs. vertical plots
- The ability to take in formula objects, just as R methods such as boxplot, lm, etc. take. This can be done in Python using patsy, but I am not very familiar with the package yet so I didn't venture there.
If I come across the need to use these features, (or if anyone would like to add them...) it might happen in the future. For now, I hope those of you missing this package from R will find this useful. Let me know if you have any feedback. Happy plotting!