Python scatter plot. Size and style of the marker

Question

I have a set of data that I want to show as a scatter plot. I want each point to be plotted as a square of size dx.

          x = [0.5,0.1,0.3]
          y = [0.2,0.7,0.8]
          z = [10.,15.,12.]
          dx = [0.05,0.2,0.1]

          scatter(x,y,c=z,s=dx,marker='s')

The problem is that the size s that the scatter function read is in points^2. What I'd like is having each point represented by a square of area dx^2, where this area is in 'real' units, the plot units. I hope you can get this point.

I also have another question. The scatter function plots the markers with a black border, how can I drop this option and have no border at all?

Fehr

Answer 1

Translate from user data coordinate system to display coordinate system.

and use edgecolors='none' to plot faces with no outlines.

import numpy as np

fig = figure()
ax = fig.add_subplot(111)
dx_in_points = np.diff(ax.transData.transform(zip([0]*len(dx), dx))) 
scatter(x,y,c=z,s=dx_in_points**2,marker='s', edgecolors='none')

Cloistral

This doesnt draw squares in plot units as the OP requested but fixed size squares that do not resize (for example by changing manually the figure frame size. – Effluence

It might be a stupid question. But how do you change the code above if dx is not an array but it's the same for every point (x,y,z). Besides, what do I really need to use add_subplot? – Fehr

How did you find the edgecolors argument? – Soche

Answer 2

I think we can do it better with a collection of patches. According to documents:

This (PatchCollection) makes it easier to assign a color map to a heterogeneous collection of patches.

This also may improve plotting speed, since PatchCollection will draw faster than a large number of patches.

Suppose you want to plot a scatter of circles with given radius in data unit:

def circles(x, y, s, c='b', vmin=None, vmax=None, **kwargs):
    """
    Make a scatter of circles plot of x vs y, where x and y are sequence 
    like objects of the same lengths. The size of circles are in data scale.

    Parameters
    ----------
    x,y : scalar or array_like, shape (n, )
        Input data
    s : scalar or array_like, shape (n, ) 
        Radius of circle in data unit.
    c : color or sequence of color, optional, default : 'b'
        `c` can be a single color format string, or a sequence of color
        specifications of length `N`, or a sequence of `N` numbers to be
        mapped to colors using the `cmap` and `norm` specified via kwargs.
        Note that `c` should not be a single numeric RGB or RGBA sequence 
        because that is indistinguishable from an array of values
        to be colormapped. (If you insist, use `color` instead.)  
        `c` can be a 2-D array in which the rows are RGB or RGBA, however. 
    vmin, vmax : scalar, optional, default: None
        `vmin` and `vmax` are used in conjunction with `norm` to normalize
        luminance data.  If either are `None`, the min and max of the
        color array is used.
    kwargs : `~matplotlib.collections.Collection` properties
        Eg. alpha, edgecolor(ec), facecolor(fc), linewidth(lw), linestyle(ls), 
        norm, cmap, transform, etc.

    Returns
    -------
    paths : `~matplotlib.collections.PathCollection`

    Examples
    --------
    a = np.arange(11)
    circles(a, a, a*0.2, c=a, alpha=0.5, edgecolor='none')
    plt.colorbar()

    License
    --------
    This code is under [The BSD 3-Clause License]
    (http://opensource.org/licenses/BSD-3-Clause)
    """
    import numpy as np
    import matplotlib.pyplot as plt
    from matplotlib.patches import Circle
    from matplotlib.collections import PatchCollection

    if np.isscalar(c):
        kwargs.setdefault('color', c)
        c = None
    if 'fc' in kwargs: kwargs.setdefault('facecolor', kwargs.pop('fc'))
    if 'ec' in kwargs: kwargs.setdefault('edgecolor', kwargs.pop('ec'))
    if 'ls' in kwargs: kwargs.setdefault('linestyle', kwargs.pop('ls'))
    if 'lw' in kwargs: kwargs.setdefault('linewidth', kwargs.pop('lw'))

    patches = [Circle((x_, y_), s_) for x_, y_, s_ in np.broadcast(x, y, s)]
    collection = PatchCollection(patches, **kwargs)
    if c is not None:
        collection.set_array(np.asarray(c))
        collection.set_clim(vmin, vmax)

    ax = plt.gca()
    ax.add_collection(collection)
    ax.autoscale_view()
    if c is not None:
        plt.sci(collection)
    return collection

All the arguments and keywords (except marker) of scatter function would work in similar way. I've write a gist including circles, ellipses and squares/rectangles. If you want a collection of other shape, you could modify it yourself.

If you want to plot a colorbar just run colorbar() or pass the returned collection object to colorbar function.

An example:

from pylab import *
figure(figsize=(6,4))
ax = subplot(aspect='equal')

#plot a set of circle
a = arange(11)
out = circles(a, a, a*0.2, c=a, alpha=0.5, ec='none')
colorbar()

#plot one circle (the lower-right one)
circles(1, 0, 0.4, 'r', ls='--', lw=5, fc='none', transform=ax.transAxes)

xlim(0,10)
ylim(0,10)

Output:

Cutlass

I'd like to use your function in an open-source project but cannot do that because by default all SO code is under CC BY-SA license. Can you explicitly state the license of your code, preferably something BSD-like? – Calen

@neo Glad to know that. I'm not familar with license, I thought it should keep be same with matplotlib, as I just wrote this code based on scatter function. So it should be PSF or something? – Cutlass

Your code snippet is not derivative works of matplotlib, therefore you can license your code under any license. I would just use BSD 3-clause, it's very common in the Python world. – Calen

@neo That's fine. I'll use BSD 3-clause. – Cutlass

Answer 3

If you want markers that resize with the figure size, you can use patches:

from matplotlib import pyplot as plt
from matplotlib.patches import Rectangle

x = [0.5, 0.1, 0.3]
y = [0.2 ,0.7, 0.8]
z = [10, 15, 12]
dx = [0.05, 0.2, 0.1]

cmap = plt.cm.hot
fig = plt.figure()
ax = fig.add_subplot(111, aspect='equal')

for x, y, c, h in zip(x, y, z, dx):
    ax.add_artist(Rectangle(xy=(x, y),
                  color=cmap(c**2),        # I did c**2 to get nice colors from your numbers
                  width=h, height=h))      # Gives a square of area h*h

plt.show()

Note that:

1. The squares are not centered at (x,y). x,y are actually the coords of the square lower left. I let it this way to simplify my code. You should use (x + dx/2, y + dx/2).
2. The color is get from the hot colormap. I used z**2 to give colors. you should also adapt this to your needs

---

Finally for your second question. You can get the border of the scatter marks out using the keyword arguments edgecolor or edgecolors. These are a matplotlib color argument or a sequence of rgba tuples, respectively. If you set the parameter to 'None', borders are not draw.

Effluence