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pyplot scatter plot marker size

In the pyplot document for scatter plot:

matplotlib.pyplot.scatter(x, y, s=20, c='b', marker='o', cmap=None, norm=None, vmin=None, vmax=None, alpha=None, linewidths=None, faceted=True, verts=None, hold=None, **kwargs)

The marker size

s: size in points^2. It is a scalar or an array of the same length as x and y.

What kind of unit is points^2? What does it mean? Does s=100 mean 10 pixel x 10 pixel?

Basically I'm trying to make scatter plots with different marker sizes, and I want to figure out what does the s number mean.

Plot logarithmic axes with matplotlib in python

I want to plot a graph with one logarithmic axis using matplotlib.

I've been reading the docs, but can't figure out the syntax. I know that it's probably something simple like 'scale=linear' in the plot arguments, but I can't seem to get it right

Sample program:

from pylab import *
import matplotlib.pyplot  as pyplot
a = [ pow(10,i) for i in range(10) ]
fig = pyplot.figure()
ax = fig.add_subplot(2,1,1)

line, = ax.plot(a, color='blue', lw=2)
show()

How do you change the size of figures drawn with matplotlib?

How do you change the size of figure drawn with matplotlib?

How to put the legend out of the plot

I have a series of 20 plots (not subplots) to be made in a single figure. I want the legend to be outside of the box. At the same time, I do not want to change the axes, as the size of the figure gets reduced. Kindly help me for the following queries:

1. I want to keep the legend box outside the plot area. (I want the legend to be outside at the right side of the plot area).
2. Is there anyway that I reduce the font size of the text inside the legend box, so that the size of the legend box will be small.

In Matplotlib, what does the argument mean in fig.add_subplot(111)?

Sometimes I come across code such as this:

import matplotlib.pyplot as plt
x = [1, 2, 3, 4, 5]
y = [1, 4, 9, 16, 25]
fig = plt.figure()
fig.add_subplot(111)
plt.scatter(x, y)
plt.show()

Which produces:

I've been reading the documentation like crazy but I can't find an explanation for the 111. sometimes I see a 212.

What does the argument of fig.add_subplot() mean?

Save plot to image file instead of displaying it using Matplotlib (so it can be used in batch scripts for example)

I am writing a quick-and-dirty script to generate plots on the fly. I am using the code below (from Matplotlib documentation) as a starting point:

from pylab import figure, axes, pie, title, show

# Make a square figure and axes
figure(1, figsize=(6, 6))
ax = axes([0.1, 0.1, 0.8, 0.8])

labels = 'Frogs', 'Hogs', 'Dogs', 'Logs'
fracs = [15, 30, 45, 10]

explode = (0, 0.05, 0, 0)
pie(fracs, explode=explode, labels=labels, autopct='%1.1f%%', shadow=True)
title('Raining Hogs and Dogs', bbox={'facecolor': '0.8', 'pad': 5})

show()  # Actually, don't show, just save to foo.png

I don't want to display the plot on a GUI, instead, I want to save the plot to a file (say foo.png) - how do I do that?

How to make IPython notebook matplotlib plot inline

I am trying to use IPython notebook on MacOS X with Python 2.7.2 and IPython 1.1.0.

I cannot get matplotlib graphics to show up inline.

import matplotlib
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline  

I have also tried %pylab inline and the ipython command line arguments --pylab=inline but this makes no difference.

x = np.linspace(0, 3*np.pi, 500)
plt.plot(x, np.sin(x**2))
plt.title('A simple chirp')
plt.show()

Instead of inline graphics, I get this:

<matplotlib.figure.Figure at 0x110b9c450>

And matplotlib.get_backend() shows that I have the 'module://IPython.kernel.zmq.pylab.backend_inline' backend.

How to change legend size with matplotlib.pyplot

Simple question here: I'm just trying to get the size of my legend using matplotlib.pyplot to be smaller (ie, the text to be smaller). The code I'm using goes something like this:

plot.figure()
plot.scatter(k,sum_cf, color = 'black', label='Sum of Cause Fractions')
plot.scatter(k, data[:, 0],  color = 'b', label = 'Dis 1: cf = .6, var = .2')
plot.scatter(k, data[:, 1],  color = 'r',  label = 'Dis 2: cf = .2, var = .1')
plot.scatter(k, data[:, 2],  color = 'g', label = 'Dis 3: cf = .1, var = .01')
plot.legend(loc=2)

Generating a PNG with matplotlib when DISPLAY is undefined

I am trying to use networkx with Python. When I run this program it get this error. Is there anything missing?

#!/usr/bin/env python

import networkx as nx
import matplotlib
import matplotlib.pyplot
import matplotlib.pyplot as plt

G=nx.Graph()
G.add_node(1)
G.add_nodes_from([2,3,4,5,6,7,8,9,10])
#nx.draw_graphviz(G)
#nx_write_dot(G, 'node.png')
nx.draw(G)
plt.savefig("/var/www/node.png")


Traceback (most recent call last):
  File "graph.py", line 13, in <module>
    nx.draw(G)
  File "/usr/lib/pymodules/python2.5/networkx/drawing/nx_pylab.py", line 124, in draw
    cf=pylab.gcf()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 276, in gcf
    return figure()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 254, in figure
    **kwargs)
  File "/usr/lib/pymodules/python2.5/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager
    window = Tk.Tk()
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1650, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

I get a different error now:

#!/usr/bin/env python

import networkx as nx
import matplotlib
import matplotlib.pyplot
import matplotlib.pyplot as plt

matplotlib.use('Agg')

G=nx.Graph()
G.add_node(1)
G.add_nodes_from([2,3,4,5,6,7,8,9,10])
#nx.draw_graphviz(G)
#nx_write_dot(G, 'node.png')
nx.draw(G)
plt.savefig("/var/www/node.png")

/usr/lib/pymodules/python2.5/matplotlib/__init__.py:835: UserWarning:  This call to matplotlib.use() has no effect
because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  if warn: warnings.warn(_use_error_msg)
Traceback (most recent call last):
  File "graph.py", line 15, in <module>
    nx.draw(G)
  File "/usr/lib/python2.5/site-packages/networkx-1.2.dev-py2.5.egg/networkx/drawing/nx_pylab.py", line 124, in draw
    cf=pylab.gcf()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 276, in gcf
    return figure()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 254, in figure
    **kwargs)
  File "/usr/lib/pymodules/python2.5/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager
    window = Tk.Tk()
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1650, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

I get a different error now:

#!/usr/bin/env python

import networkx as nx
import matplotlib
import matplotlib.pyplot
import matplotlib.pyplot as plt

matplotlib.use('Agg')

G=nx.Graph()
G.add_node(1)
G.add_nodes_from([2,3,4,5,6,7,8,9,10])
#nx.draw_graphviz(G)
#nx_write_dot(G, 'node.png')
nx.draw(G)
plt.savefig("/var/www/node.png")

/usr/lib/pymodules/python2.5/matplotlib/__init__.py:835: UserWarning:  This call to matplotlib.use() has no effect
because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  if warn: warnings.warn(_use_error_msg)
Traceback (most recent call last):
  File "graph.py", line 15, in <module>
    nx.draw(G)
  File "/usr/lib/python2.5/site-packages/networkx-1.2.dev-py2.5.egg/networkx/drawing/nx_pylab.py", line 124, in draw
    cf=pylab.gcf()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 276, in gcf
    return figure()
  File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 254, in figure
    **kwargs)
  File "/usr/lib/pymodules/python2.5/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager
    window = Tk.Tk()
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1650, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

Ubuntu running `pip install` gives error 'The following required packages can not be built: * freetype'

When performing pip install -r requirements.txt, I get the following error during the stage where it is installing matplotlib:

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [not found. pip may install it below.]
              dateutil: yes [dateutil was not found. It is required for date
                        axis support. pip/easy_install may attempt to
                        install it after matplotlib.]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [pyparsing was not found. It is required for
                        mathtext support. pip/easy_install may attempt to
                        install it after matplotlib.]
                 pycxx: yes [Couldn't import.  Using local copy.]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: no  [pkg-config information for 'freetype2' could
                        not be found.]

...

The following required packages can not be built:

                    * freetype

Shouldn't pip install -r requirements.txt also install freetype? How should freetype be installed in Ubuntu 12.04 so it works with matplotlib?

What is the difference between pylab and pyplot? [duplicate]

What is the difference between matplotlib.pyplot and matplotlib.pylab?

Which is preferred for what usage?

I am a little confused, because it seems like independent from which I import, I can do the same things. What am I missing?

Pip install Matplotlib error with virtualenv

I am trying to install matplotlib in a new virtualenv.

When I do:

pip install matplotlib

or

pip install http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.1.0/matplotlib-1.1.0.tar.gz

I get this error:

building 'matplotlib._png' extension

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC -  DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/include -I/usr/include -I. -I/home/sam/django-projects/datazone/local/lib/python2.7/site-packages/numpy/core/include -I. -I/usr/include/python2.7 -c src/_png.cpp -o build/temp.linux-x86_64-2.7/src/_png.o

src/_png.cpp:10:20: fatal error: png.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

Anyone have an idea what is going on?

Any help much appreciated.

How do I set figure title and axes labels font size in matplotlib?

I am creating a figure in matplotlib like this:

from matplotlib import pyplot as plt    

fig = plt.figure()
plt.plot(data)
fig.suptitle('test title')
plt.xlabel('xlabel')
plt.ylabel('ylabel')
fig.savefig('test.jpg')

I want to specify font sizes for the figure title and the axis labels. I need all three to be different font sizes, so setting a global font size (mpl.rcParams['font.size']=x) is not what I want. How do I set font sizes for the figure title and the axis labels individually?

Generating matplotlib graphs without a running X server [duplicate]

Matplotlib seems to require the $DISPLAY environment variable which means a running X server.
Some web hosting services do not allow a running X server session.
Is there a way to generate graphs using matplotlib without a running X server?

[username@hostname ~]$ python2.6
Python 2.6.5 (r265:79063, Nov 23 2010, 02:02:03)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
>>> fig = plt.figure()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/username/lib/python2.6/matplotlib-1.0.1-py2.6-linux-i686.egg/matplotlib/pyplot.py", line 270, in figure
    **kwargs)
  File "/home/username/lib/python2.6/matplotlib-1.0.1-py2.6-linux-i686.egg/matplotlib/backends/backend_tkagg.py", line 80, in new_figure_manager
    window = Tk.Tk()
  File "/usr/local/lib/python2.6/lib-tk/Tkinter.py", line 1643, in __init__
    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
>>>

Generate a heatmap in MatPlotLib using a scatter data set

I have a set of X,Y data points (about 10k) that are easy to plot as a scatter plot but that I would like to represent as a heatmap.

I looked through the examples in MatPlotLib and they all seem to already start with heatmap cell values to generate the image.

Is there a method that converts a bunch of x,y, all different, to a heatmap (where zones with higher frequency of x,y would be "warmer")?