Thread: [Matplotlib-users] starting with pplots

Hi,

I am a new user of matplotlib so maybe my question is elementary, but 
have not been able to find an answer to my problem in the archive.

I would like to make a 2D plot of colored points of 3D data (clusters). 
My data looks like this:

11837.2120    -0.0858    2.0000
23975.2120    -0.0672    2.0000
37609.2120    -0.0306    2.0000
53263.9800    -0.0690    2.0000
72106.6760    0.2708     1.0000
92674.6760    -0.0129    3.0000
116758.676    -0.1245    3.0000
...

So I need to plot the first and second column as points on the x-y axis 
and color the points according to the numbers in the third column (which 
are integers ranging from 1 to5).

I'd appreciate any help. I realize something so typical should be 
somewhere in the documentation but I was not able to find it.

Thanks,
Paul

2010/12/19 Pawel <pa...@gm...>:
> Hi,
>
> I am a new user of matplotlib so maybe my question is elementary, but
> have not been able to find an answer to my problem in the archive.
>
> I would like to make a 2D plot of colored points of 3D data (clusters).
> My data looks like this:
>
> 11837.2120    -0.0858    2.0000
> 23975.2120    -0.0672    2.0000
> 37609.2120    -0.0306    2.0000
> 53263.9800    -0.0690    2.0000
> 72106.6760    0.2708     1.0000
> 92674.6760    -0.0129    3.0000
> 116758.676    -0.1245    3.0000
> ...
>
> So I need to plot the first and second column as points on the x-y axis
> and color the points according to the numbers in the third column (which
> are integers ranging from 1 to5).
>
> I'd appreciate any help. I realize something so typical should be
> somewhere in the documentation but I was not able to find it.

Try this:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
x, y, z = np.loadtxt('data.txt', unpack=True)
cmap = ListedColormap(['b', 'g', 'r', 'c', 'm'])
plt.scatter(x, y, c=z, cmap=cmap, vmin=1, vmax=5)
plt.show()

You'll need to use a single space as column delimiter in your data
file or deal with more loadtxt arguments.

If your z data were color specifications you could just use
plt.scatter(x, y, c=z) as stated in the scatter docstring. Converting
arbitrary data to color specifications is the non trivial issue here.
You can write your own code to do this or use colormaps.


Goyo

Pawel, on 2010-12-18 20:04,  wrote:
> Hi,
> 
> I am a new user of matplotlib so maybe my question is elementary, but 
> have not been able to find an answer to my problem in the archive.
> 
> I would like to make a 2D plot of colored points of 3D data (clusters). 
> My data looks like this:
> 
> 11837.2120    -0.0858    2.0000
> 23975.2120    -0.0672    2.0000
> 37609.2120    -0.0306    2.0000
> 53263.9800    -0.0690    2.0000
> 72106.6760    0.2708     1.0000
> 92674.6760    -0.0129    3.0000
> 116758.676    -0.1245    3.0000
> ...
> 
> So I need to plot the first and second column as points on the x-y axis 
> and color the points according to the numbers in the third column (which 
> are integers ranging from 1 to5).
> 
> I'd appreciate any help. I realize something so typical should be 
> somewhere in the documentation but I was not able to find it.

Hi Paul,
welcome to matplotlib! So you need to read in those columns
somehow (as numpy arrays, or lists), but once you've got that,
it's just a matter of initiating a 3d plot, and calling scatter
with the three columns.

take a look at this example and it's source code:
http://matplotlib.sourceforge.net/mpl_toolkits/mplot3d/tutorial.html#scatter-plots

for your purposes, the code will be something like:

  from mpl_toolkits.mplot3d import Axes3D
  import matplotlib.pyplot as plt
  fig = plt.figure()
  ax = fig.add_subplot(111, projection='3d')
  ax.scatter(x,y,z)

best,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Pawel Janowski, on 2010-12-23 10:09,  wrote:
> Hi Pavel,
> 
> Thanks for your help. Matplotlib seems to be a really cool tool. Your
> response almost answered my question. What I want is for the 3D plot to be
> 2D. I mean the z-axis can only take on 5 discreet values so I don't want to
> visualize 3 dimensions but just two with the data points colored five
> different colors depending on the z value. 

Pawel,

(I'm replying back to the list, so that others may benefit -
hello there, search engine visitors from the future!)

In that case, you can either follow Goya's suggestion - if you
only want to draw points. scatter will actually rescale the color
values you give to whatever colormap you're using - and for your
case, with just five z values in range(1,6), I found a slight
tweak to the 'hsv' colormap does the trick.

  from numpy.random import rand, randint
  import matplotlib.pyplot as plt
  x,y = rand(2,100)
  z = randint(1,6,100)
  plt.scatter(x,y,c=z, vmin=-1, cmap=plt.get_cmap('hsv'))

You can see the built-in colormaps here:
http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html

and as Goyo showed, it's pretty easy to make a new one.

If you want more control, such as changing the shape of the
marker, not just the color, or if there's some order to your points
that you want to also see (for example, draw lines between points
of the same z value) - you can use a boolean mask. 

  from numpy.random import rand, randint
  import matplotlib.pyplot as plt
  x,y = rand(2,100)
  z = randint(1,6,100)
  for i,c,m in zip(range(1,6),'rgbmk', 'odp*s'):
      mask = z==i
      plt.plot(x[mask],y[mask], color=c, marker=m)

hope that helps,
-- 
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 

Hey guys,

Thank you so much for your clear answers which have been very helpful!

Pawel

-----Wiadomość oryginalna-----
Od: Paul Ivanov [mailto:piv...@gm...] 
Wysłano: Thursday, December 23, 2010 3:03 PM
Do: mat...@li...
DW: Pawel Janowski
Temat: Re: ODP: [Matplotlib-users] starting with pplots

Pawel Janowski, on 2010-12-23 10:09,  wrote:
> Hi Pavel,
> 
> Thanks for your help. Matplotlib seems to be a really cool tool. Your 
> response almost answered my question. What I want is for the 3D plot 
> to be 2D. I mean the z-axis can only take on 5 discreet values so I 
> don't want to visualize 3 dimensions but just two with the data points 
> colored five different colors depending on the z value.

Pawel,

(I'm replying back to the list, so that others may benefit - hello there,
search engine visitors from the future!)

In that case, you can either follow Goya's suggestion - if you only want to
draw points. scatter will actually rescale the color values you give to
whatever colormap you're using - and for your case, with just five z values
in range(1,6), I found a slight tweak to the 'hsv' colormap does the trick.

  from numpy.random import rand, randint
  import matplotlib.pyplot as plt
  x,y = rand(2,100)
  z = randint(1,6,100)
  plt.scatter(x,y,c=z, vmin=-1, cmap=plt.get_cmap('hsv'))

You can see the built-in colormaps here:
http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.htm
l

and as Goyo showed, it's pretty easy to make a new one.

If you want more control, such as changing the shape of the marker, not just
the color, or if there's some order to your points that you want to also see
(for example, draw lines between points of the same z value) - you can use a
boolean mask. 

  from numpy.random import rand, randint
  import matplotlib.pyplot as plt
  x,y = rand(2,100)
  z = randint(1,6,100)
  for i,c,m in zip(range(1,6),'rgbmk', 'odp*s'):
      mask = z==i
      plt.plot(x[mask],y[mask], color=c, marker=m)

hope that helps,
--
Paul Ivanov
314 address only used for lists,  off-list direct email at:
http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7