pybeeswarm
Beeswarm plots for python. Inspired by R beeswarm plots
Install
The easiest way to install pybeeswarm is using pip:
sudo pip install pybeeswarm
To install the latest version on github, simply do:
git clone https://github.com/mgymrek/pybeeswarm.git
cd pybeeswarm
sudo python setup.py install
To test that it worked, open up python and check that import beeswarm doesn't give you any errors.
Requirements
This package requires:
- matplotlib
- numpy
- pandas
Basic usage
There is only one function, beeswarm:
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"])
