Hi all,
I needed to make bean plots (see
http://www.jstatsoft.org/v28/c01/paper ) so I made a function to plot
them by tuning the violin plot code from here:
http://pyinsci.blogspot.com/2009/09/violin-plot-with-matplotlib.html
Please see the attached file if interested.
Is there a repository where this kind of additional plot functions
could be submitted? The violinplot function needs scipy, so it's maybe
matplotlib itself is out of the question?
Best,
Teemu
# Author: Teemu Ikonen <tpiko...@gmail.com>
# Based on code by Flavio Codeco Coelho,
# http://pyinsci.blogspot.com/2009/09/violin-plot-with-matplotlib.html
import numpy as np
from matplotlib.pyplot import figure, show
from scipy.stats import gaussian_kde
from numpy.random import normal
def violinplot(ax, data, pos, bp=False, cut=False):
"""Make a violin plot of each dataset in the `data` sequence.
"""
dist = np.max(pos)-np.min(pos)
w = min(0.15*max(dist,1.0),0.5)
for d,p in zip(data,pos):
k = gaussian_kde(d) #calculates the kernel density
s = 0.0
if not cut:
s = 1.5*np.std(d) #FIXME: magic constant 1.5
m = k.dataset.min() - s #lower bound of violin
M = k.dataset.max() + s #upper bound of violin
x = np.linspace(m, M, 100) # support for violin
v = k.evaluate(x) #violin profile (density curve)
v = w*v/v.max() #scaling the violin to the available space
ax.fill_betweenx(x,-v+p,v+p,facecolor='y',alpha=0.3)
if bp:
ax.boxplot(data,notch=1,positions=pos,vert=1)
def stripchart(ax, data, pos, mean=False, median=False, width=None):
"""Plot samples given in `data` as horizontal lines.
Keyword arguments:
mean: plot mean of each dataset as a thicker line if True
median: plot median of each dataset as a dot if True.
width: Horizontal width of a single dataset plot.
"""
if width:
w = width
else:
dist = np.max(pos)-np.min(pos)
w = min(0.15*max(dist,1.0),0.5)
for d,p in zip(data,pos):
hw = w/2.0
ax.hlines(d, p-hw, p+hw, lw=0.5)
if mean:
ax.hlines(np.mean(d), p-w, p+w, lw=1.0, color='b')
if median:
ax.plot(p, np.median(d), 'o', color='r')
def beanplot(ax, data, pos, mean=True, median=True, cut=False):
"""Make a bean plot of each dataset in the `data` sequence.
Reference: http://www.jstatsoft.org/v28/c01/paper
"""
#FIXME: Implement also the asymmetric beanplot
dist = np.max(pos)-np.min(pos)
w = min(0.15*max(dist,1.0),0.5)
stripchart(ax, data, pos, mean, median, 0.8*w)
violinplot(ax, data, pos, False, cut)
if __name__=="__main__":
pos = range(5)
data = [normal(size=100) for i in pos]
fig=figure()
ax = fig.add_subplot(111)
beanplot(ax,data,pos)
show()
------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today. Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
