Display two Sympy plots as two Matplotlib subplots - matplotlib

This code
from sympy import *
x=Symbol('x')
p1 = plot(x**2,(x,-2,2))
p2 = plot(x**3,(x,-2,2))
results in two separate plots.
Instead of two separate plots, I want to display them with matplotlib as subplots:
import matplotlib.pyplot as plt
fig = plt.figure()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
plt.show()
How can I add p1 and p2, so that they are displayed as subplots inside the matplotlib figure?

The problem is that sympy Plot creates its own figure and axes. It is not meant to draw to an existing axes.
You may however replace the axes the plot is drawn to by an existing axes prior to showing the sympy plot.
from sympy import Symbol,plot
import matplotlib.pyplot as plt
def move_sympyplot_to_axes(p, ax):
backend = p.backend(p)
backend.ax = ax
backend.process_series()
backend.ax.spines['right'].set_color('none')
backend.ax.spines['bottom'].set_position('zero')
backend.ax.spines['top'].set_color('none')
plt.close(backend.fig)
x=Symbol('x')
p1 = plot(x**2,(x,-2,2), show=False)
p2 = plot(x**3,(x,-2,2), show=False)
fig, (ax,ax2) = plt.subplots(ncols=2)
move_sympyplot_to_axes(p1, ax)
move_sympyplot_to_axes(p2, ax2)
plt.show()

My solution does not add p1, p2 to the subplots directly. But (x,y) coordinates from them are captured and used instead.
import matplotlib.pyplot as plt
from sympy import symbols
import numpy as np
from sympy import symbols
from sympy.plotting import plot
# part 1
# uses symbolic plot of functions
x = symbols('x')
#p1, p2 = plot(x**2, x**3, (x, -2, 2))
# this plot will not show ...
# only produce 2 curves
p1, p2 = plot((x**2, (x, -2, 2)), \
(x**3, (x, -2, 2)), \
show=False)
# collect (x,y)'s of the unseen curves
x1y1 = p1.get_points() # array of 2D
x2y2 = p2.get_points()
# part 2
# uses regular matplotlib to plot the data
fig = plt.figure(figsize=(8, 5))
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
# do subplot 1
ax1.plot(x1y1[0], x1y1[1], 'g') # plot x**2 in green
ax1.set_xlim([-2, 2])
ax1.set_xlabel('X1')
ax1.set_ylabel('Y1')
ax1.set_title('Line1') # destroyed by another .title(); axis metho1
# do subplot 2
ax2.plot(x2y2[0], x2y2[1], 'r') # plot x**3 in red
ax2.set_xlim([-2, 2])
ax2.set_xlabel('X2')
ax2.set_ylabel('Y2')
ax2.set_title('Line2')
fig.subplots_adjust(wspace=0.4) # set space between subplots
plt.show()
The resulting plot:

You can simply use a plotgrid to get 2 or more plots in one figure.
See also: sympy.plotting.PlotGrid()
Here's a working example:
import sympy as sp
from matplotlib import pyplot as plt
# define functions
x = symbols('x')
f = sin(x)
g = cos(x)
# create separate plots
p1 = plot(f, show=False, xlim=(-pi, pi), line_color='blue', legend=True)
p2 = plot(g, show=False, xlim=(-pi, pi), line_color='red', legend=True)
# create a plotgrid with 2 rows and 1 column
plotgrid = sp.plotting.PlotGrid(2, 1, p1, p2, show=False, size=(5., 3.5))
plotgrid.show()
Resulting plot:

Related

LineCollections for few lines with a single colorbar

I'm trying to plot some lines using LineCollection in a plot. Each of these lines is needed to be mapped to colorbar whose range varies for each lines. I tried as explained here
https://matplotlib.org/stable/gallery/lines_bars_and_markers/multicolored_line.html?highlight=line%20collection
In the end, I want a single colorbar, for let's say three lines, covering all ranges. However, the colorbar is set for the last line values. So I looked here
https://matplotlib.org/stable/gallery/images_contours_and_fields/multi_image.html
But I'm not being successful since I'm quite new to Matplotlib. I paste my code below. I'm just trying to map the value of the lines (also shown on y-axis) in a colorbar for all three lines. Any help is appreciated.
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib import colors
lineSegments = [np.linspace(0,1,10),
np.linspace(0,5,10),
np.linspace(0,2,10)]
xVec = np.linspace(0,1,10)
fig, ax = plt.subplots()
for i in range(0, len(lineSegments)):
cValue = np.linspace( min(lineSegments[i]), max(lineSegments[i]) )
norm = colors.Normalize(vmin=cValue.min(), vmax=cValue.max() )
Points = np.array([xVec, lineSegments[i]]).T.reshape(-1,1,2)
PointSegments = np.concatenate([Points[:-1],Points[1:]], axis=1)
lc = LineCollection(PointSegments, cmap=plt.get_cmap('jet'),
norm=norm)
#plt.gca().add_collection(lc)
ax.add_collection(lc)
ax.set_xlim( min(xVec), max(xVec) )
ax.set_ylim( np.amin(lineSegments), np.amax(lineSegments) )
lc.set_array(cValue)
fig.colorbar(lc)
def update(changed_lines):
for i in range(0, len(lineSegments)):
if (changed_lines.get_cmap() != lc.get_cmap()
or changed_lines.get_clim() != lc.get_clim()):
lc.set_cmap(changed_lines.get_cmap())
lc.set_clim(changed_lines.get_clim())
for i in range(0, len(lineSegments)):
lc.callbacksSM.connect('changed',update)
plt.show()
I have modified your code. Essentially what you need to do is create a norm instance for the entire dataset and then assign color values to the segments according to the colormap you have with the given norm. You can then pass it to the colorbar accordingly.
As such
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib import colors
lineSegments = [np.linspace(0,1,10),
np.linspace(0,5,10),
np.linspace(0,2,10)]
xVec = np.linspace(0,1,10)
fig, ax = plt.subplots()
norm = colors.Normalize(vmin=min([ i.min() for i in lineSegments ]),
vmax=max([i.max() for i in lineSegments]))
cmap = plt.get_cmap('jet')
for i in range(0, len(lineSegments)):
cValue = norm(lineSegments[i])
c = cmap(cValue)
Points = np.array([xVec, lineSegments[i]]).T.reshape(-1,1,2)
PointSegments = np.concatenate([Points[:-1],Points[1:]], axis=1)
lc = LineCollection(PointSegments, cmap=cmap,
norm=norm, colors = c)
#plt.gca().add_collection(lc)
ax.add_collection(lc)
ax.set_xlim( min(xVec), max(xVec) )
ax.set_ylim( np.amin(lineSegments), np.amax(lineSegments) )
# lc.set_array(cValue)
sc = plt.cm.ScalarMappable(norm = norm, cmap = cmap)
fig.colorbar(sc)
def update(changed_lines):
for i in range(0, len(lineSegments)):
if (changed_lines.get_cmap() != lc.get_cmap()
or changed_lines.get_clim() != lc.get_clim()):
lc.set_cmap(changed_lines.get_cmap())
lc.set_clim(changed_lines.get_clim())
for i in range(0, len(lineSegments)):
lc.callbacksSM.connect('changed',update)
plt.show()

How to have only 1 shared colorbar for multiple plots [duplicate]

I've spent entirely too long researching how to get two subplots to share the same y-axis with a single colorbar shared between the two in Matplotlib.
What was happening was that when I called the colorbar() function in either subplot1 or subplot2, it would autoscale the plot such that the colorbar plus the plot would fit inside the 'subplot' bounding box, causing the two side-by-side plots to be two very different sizes.
To get around this, I tried to create a third subplot which I then hacked to render no plot with just a colorbar present.
The only problem is, now the heights and widths of the two plots are uneven, and I can't figure out how to make it look okay.
Here is my code:
from __future__ import division
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import patches
from matplotlib.ticker import NullFormatter
# SIS Functions
TE = 1 # Einstein radius
g1 = lambda x,y: (TE/2) * (y**2-x**2)/((x**2+y**2)**(3/2))
g2 = lambda x,y: -1*TE*x*y / ((x**2+y**2)**(3/2))
kappa = lambda x,y: TE / (2*np.sqrt(x**2+y**2))
coords = np.linspace(-2,2,400)
X,Y = np.meshgrid(coords,coords)
g1out = g1(X,Y)
g2out = g2(X,Y)
kappaout = kappa(X,Y)
for i in range(len(coords)):
for j in range(len(coords)):
if np.sqrt(coords[i]**2+coords[j]**2) <= TE:
g1out[i][j]=0
g2out[i][j]=0
fig = plt.figure()
fig.subplots_adjust(wspace=0,hspace=0)
# subplot number 1
ax1 = fig.add_subplot(1,2,1,aspect='equal',xlim=[-2,2],ylim=[-2,2])
plt.title(r"$\gamma_{1}$",fontsize="18")
plt.xlabel(r"x ($\theta_{E}$)",fontsize="15")
plt.ylabel(r"y ($\theta_{E}$)",rotation='horizontal',fontsize="15")
plt.xticks([-2.0,-1.5,-1.0,-0.5,0,0.5,1.0,1.5])
plt.xticks([-2.0,-1.5,-1.0,-0.5,0,0.5,1.0,1.5])
plt.imshow(g1out,extent=(-2,2,-2,2))
plt.axhline(y=0,linewidth=2,color='k',linestyle="--")
plt.axvline(x=0,linewidth=2,color='k',linestyle="--")
e1 = patches.Ellipse((0,0),2,2,color='white')
ax1.add_patch(e1)
# subplot number 2
ax2 = fig.add_subplot(1,2,2,sharey=ax1,xlim=[-2,2],ylim=[-2,2])
plt.title(r"$\gamma_{2}$",fontsize="18")
plt.xlabel(r"x ($\theta_{E}$)",fontsize="15")
ax2.yaxis.set_major_formatter( NullFormatter() )
plt.axhline(y=0,linewidth=2,color='k',linestyle="--")
plt.axvline(x=0,linewidth=2,color='k',linestyle="--")
plt.imshow(g2out,extent=(-2,2,-2,2))
e2 = patches.Ellipse((0,0),2,2,color='white')
ax2.add_patch(e2)
# subplot for colorbar
ax3 = fig.add_subplot(1,1,1)
ax3.axis('off')
cbar = plt.colorbar(ax=ax2)
plt.show()
Just place the colorbar in its own axis and use subplots_adjust to make room for it.
As a quick example:
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.subplots_adjust(right=0.8)
cbar_ax = fig.add_axes([0.85, 0.15, 0.05, 0.7])
fig.colorbar(im, cax=cbar_ax)
plt.show()
Note that the color range will be set by the last image plotted (that gave rise to im) even if the range of values is set by vmin and vmax. If another plot has, for example, a higher max value, points with higher values than the max of im will show in uniform color.
You can simplify Joe Kington's code using the axparameter of figure.colorbar() with a list of axes.
From the documentation:
ax
None | parent axes object(s) from which space for a new colorbar axes will be stolen. If a list of axes is given they will all be resized to make room for the colorbar axes.
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
This solution does not require manual tweaking of axes locations or colorbar size, works with multi-row and single-row layouts, and works with tight_layout(). It is adapted from a gallery example, using ImageGrid from matplotlib's AxesGrid Toolbox.
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import ImageGrid
# Set up figure and image grid
fig = plt.figure(figsize=(9.75, 3))
grid = ImageGrid(fig, 111, # as in plt.subplot(111)
nrows_ncols=(1,3),
axes_pad=0.15,
share_all=True,
cbar_location="right",
cbar_mode="single",
cbar_size="7%",
cbar_pad=0.15,
)
# Add data to image grid
for ax in grid:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
# Colorbar
ax.cax.colorbar(im)
ax.cax.toggle_label(True)
#plt.tight_layout() # Works, but may still require rect paramater to keep colorbar labels visible
plt.show()
Using make_axes is even easier and gives a better result. It also provides possibilities to customise the positioning of the colorbar.
Also note the option of subplots to share x and y axes.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
fig, axes = plt.subplots(nrows=2, ncols=2, sharex=True, sharey=True)
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
cax,kw = mpl.colorbar.make_axes([ax for ax in axes.flat])
plt.colorbar(im, cax=cax, **kw)
plt.show()
As a beginner who stumbled across this thread, I'd like to add a python-for-dummies adaptation of abevieiramota's very neat answer (because I'm at the level that I had to look up 'ravel' to work out what their code was doing):
import numpy as np
import matplotlib.pyplot as plt
fig, ((ax1,ax2,ax3),(ax4,ax5,ax6)) = plt.subplots(2,3)
axlist = [ax1,ax2,ax3,ax4,ax5,ax6]
first = ax1.imshow(np.random.random((10,10)), vmin=0, vmax=1)
third = ax3.imshow(np.random.random((12,12)), vmin=0, vmax=1)
fig.colorbar(first, ax=axlist)
plt.show()
Much less pythonic, much easier for noobs like me to see what's actually happening here.
Shared colormap and colorbar
This is for the more complex case where the values are not just between 0 and 1; the cmap needs to be shared instead of just using the last one.
import numpy as np
from matplotlib.colors import Normalize
import matplotlib.pyplot as plt
import matplotlib.cm as cm
fig, axes = plt.subplots(nrows=2, ncols=2)
cmap=cm.get_cmap('viridis')
normalizer=Normalize(0,4)
im=cm.ScalarMappable(norm=normalizer)
for i,ax in enumerate(axes.flat):
ax.imshow(i+np.random.random((10,10)),cmap=cmap,norm=normalizer)
ax.set_title(str(i))
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
As pointed out in other answers, the idea is usually to define an axes for the colorbar to reside in. There are various ways of doing so; one that hasn't been mentionned yet would be to directly specify the colorbar axes at subplot creation with plt.subplots(). The advantage is that the axes position does not need to be manually set and in all cases with automatic aspect the colorbar will be exactly the same height as the subplots. Even in many cases where images are used the result will be satisfying as shown below.
When using plt.subplots(), the use of gridspec_kw argument allows to make the colorbar axes much smaller than the other axes.
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(5.5,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
Example:
import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(5.5,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
fig.subplots_adjust(wspace=0.3)
im = ax.imshow(np.random.rand(11,8), vmin=0, vmax=1)
im2 = ax2.imshow(np.random.rand(11,8), vmin=0, vmax=1)
ax.set_ylabel("y label")
fig.colorbar(im, cax=cax)
plt.show()
This works well, if the plots' aspect is autoscaled or the images are shrunk due to their aspect in the width direction (as in the above). If, however, the images are wider then high, the result would look as follows, which might be undesired.
A solution to fix the colorbar height to the subplot height would be to use mpl_toolkits.axes_grid1.inset_locator.InsetPosition to set the colorbar axes relative to the image subplot axes.
import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)
from mpl_toolkits.axes_grid1.inset_locator import InsetPosition
fig, (ax, ax2, cax) = plt.subplots(ncols=3,figsize=(7,3),
gridspec_kw={"width_ratios":[1,1, 0.05]})
fig.subplots_adjust(wspace=0.3)
im = ax.imshow(np.random.rand(11,16), vmin=0, vmax=1)
im2 = ax2.imshow(np.random.rand(11,16), vmin=0, vmax=1)
ax.set_ylabel("y label")
ip = InsetPosition(ax2, [1.05,0,0.05,1])
cax.set_axes_locator(ip)
fig.colorbar(im, cax=cax, ax=[ax,ax2])
plt.show()
New in matplotlib 3.4.0
Shared colorbars can now be implemented using subfigures:
New Figure.subfigures and Figure.add_subfigure allow ... localized figure artists (e.g., colorbars and suptitles) that only pertain to each subfigure.
The matplotlib gallery includes demos on how to plot subfigures.
Here is a minimal example with 2 subfigures, each with a shared colorbar:
fig = plt.figure(constrained_layout=True)
(subfig_l, subfig_r) = fig.subfigures(nrows=1, ncols=2)
axes_l = subfig_l.subplots(nrows=1, ncols=2, sharey=True)
for ax in axes_l:
im = ax.imshow(np.random.random((10, 10)), vmin=0, vmax=1)
# shared colorbar for left subfigure
subfig_l.colorbar(im, ax=axes_l, location='bottom')
axes_r = subfig_r.subplots(nrows=3, ncols=1, sharex=True)
for ax in axes_r:
mesh = ax.pcolormesh(np.random.randn(30, 30), vmin=-2.5, vmax=2.5)
# shared colorbar for right subfigure
subfig_r.colorbar(mesh, ax=axes_r)
The solution of using a list of axes by abevieiramota works very well until you use only one row of images, as pointed out in the comments. Using a reasonable aspect ratio for figsize helps, but is still far from perfect. For example:
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(9.75, 3))
for ax in axes.flat:
im = ax.imshow(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.ravel().tolist())
plt.show()
The colorbar function provides the shrink parameter which is a scaling factor for the size of the colorbar axes. It does require some manual trial and error. For example:
fig.colorbar(im, ax=axes.ravel().tolist(), shrink=0.75)
To add to #abevieiramota's excellent answer, you can get the euqivalent of tight_layout with constrained_layout. You will still get large horizontal gaps if you use imshow instead of pcolormesh because of the 1:1 aspect ratio imposed by imshow.
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=2, constrained_layout=True)
for ax in axes.flat:
im = ax.pcolormesh(np.random.random((10,10)), vmin=0, vmax=1)
fig.colorbar(im, ax=axes.flat)
plt.show()
I noticed that almost every solution posted involved ax.imshow(im, ...) and did not normalize the colors displayed to the colorbar for the multiple subfigures. The im mappable is taken from the last instance, but what if the values of the multiple im-s are different? (I'm assuming these mappables are treated in the same way that the contour-sets and surface-sets are treated.) I have an example using a 3d surface plot below that creates two colorbars for a 2x2 subplot (one colorbar per one row). Although the question asks explicitly for a different arrangement, I think the example helps clarify some things. I haven't found a way to do this using plt.subplots(...) yet because of the 3D axes unfortunately.
If only I could position the colorbars in a better way... (There is probably a much better way to do this, but at least it should be not too difficult to follow.)
import matplotlib
from matplotlib import cm
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
cmap = 'plasma'
ncontours = 5
def get_data(row, col):
""" get X, Y, Z, and plot number of subplot
Z > 0 for top row, Z < 0 for bottom row """
if row == 0:
x = np.linspace(1, 10, 10, dtype=int)
X, Y = np.meshgrid(x, x)
Z = np.sqrt(X**2 + Y**2)
if col == 0:
pnum = 1
else:
pnum = 2
elif row == 1:
x = np.linspace(1, 10, 10, dtype=int)
X, Y = np.meshgrid(x, x)
Z = -np.sqrt(X**2 + Y**2)
if col == 0:
pnum = 3
else:
pnum = 4
print("\nPNUM: {}, Zmin = {}, Zmax = {}\n".format(pnum, np.min(Z), np.max(Z)))
return X, Y, Z, pnum
fig = plt.figure()
nrows, ncols = 2, 2
zz = []
axes = []
for row in range(nrows):
for col in range(ncols):
X, Y, Z, pnum = get_data(row, col)
ax = fig.add_subplot(nrows, ncols, pnum, projection='3d')
ax.set_title('row = {}, col = {}'.format(row, col))
fhandle = ax.plot_surface(X, Y, Z, cmap=cmap)
zz.append(Z)
axes.append(ax)
## get full range of Z data as flat list for top and bottom rows
zz_top = zz[0].reshape(-1).tolist() + zz[1].reshape(-1).tolist()
zz_btm = zz[2].reshape(-1).tolist() + zz[3].reshape(-1).tolist()
## get top and bottom axes
ax_top = [axes[0], axes[1]]
ax_btm = [axes[2], axes[3]]
## normalize colors to minimum and maximum values of dataset
norm_top = matplotlib.colors.Normalize(vmin=min(zz_top), vmax=max(zz_top))
norm_btm = matplotlib.colors.Normalize(vmin=min(zz_btm), vmax=max(zz_btm))
cmap = cm.get_cmap(cmap, ncontours) # number of colors on colorbar
mtop = cm.ScalarMappable(cmap=cmap, norm=norm_top)
mbtm = cm.ScalarMappable(cmap=cmap, norm=norm_btm)
for m in (mtop, mbtm):
m.set_array([])
# ## create cax to draw colorbar in
# cax_top = fig.add_axes([0.9, 0.55, 0.05, 0.4])
# cax_btm = fig.add_axes([0.9, 0.05, 0.05, 0.4])
cbar_top = fig.colorbar(mtop, ax=ax_top, orientation='vertical', shrink=0.75, pad=0.2) #, cax=cax_top)
cbar_top.set_ticks(np.linspace(min(zz_top), max(zz_top), ncontours))
cbar_btm = fig.colorbar(mbtm, ax=ax_btm, orientation='vertical', shrink=0.75, pad=0.2) #, cax=cax_btm)
cbar_btm.set_ticks(np.linspace(min(zz_btm), max(zz_btm), ncontours))
plt.show()
plt.close(fig)
## orientation of colorbar = 'horizontal' if done by column
This topic is well covered but I still would like to propose another approach in a slightly different philosophy.
It is a bit more complex to set-up but it allow (in my opinion) a bit more flexibility. For example, one can play with the respective ratios of each subplots / colorbar:
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.gridspec import GridSpec
# Define number of rows and columns you want in your figure
nrow = 2
ncol = 3
# Make a new figure
fig = plt.figure(constrained_layout=True)
# Design your figure properties
widths = [3,4,5,1]
gs = GridSpec(nrow, ncol + 1, figure=fig, width_ratios=widths)
# Fill your figure with desired plots
axes = []
for i in range(nrow):
for j in range(ncol):
axes.append(fig.add_subplot(gs[i, j]))
im = axes[-1].pcolormesh(np.random.random((10,10)))
# Shared colorbar
axes.append(fig.add_subplot(gs[:, ncol]))
fig.colorbar(im, cax=axes[-1])
plt.show()
The answers above are great, but most of them use the fig.colobar() method applied to a fig object. This example shows how to use the plt.colobar() function, applied directly to pyplot:
def shared_colorbar_example():
fig, axs = plt.subplots(nrows=3, ncols=3)
for ax in axs.flat:
plt.sca(ax)
color = np.random.random((10))
plt.scatter(range(10), range(10), c=color, cmap='viridis', vmin=0, vmax=1)
plt.colorbar(ax=axs.ravel().tolist(), shrink=0.6)
plt.show()
shared_colorbar_example()
Since most answers above demonstrated usage on 2D matrices, I went with a simple scatter plot. The shrink keyword is optional and resizes the colorbar.
If vmin and vmax are not specified this approach will automatically analyze all of the subplots for the minimum and maximum value to be used on the colorbar. The above approaches when using fig.colorbar(im) scan only the image passed as argument for min and max values of the colorbar.
Result:

matplotlib contour works while contourf fails on the same data set

I'm trying to vizualize a function of two variable using contour and contourf functions of matlotlib. Using the same data, contour works perfectly but contourf produces defective images. What is the reason for that?
from numpy import exp, pi
import numpy as np
# function to be plotted
def R(n0,n1,y,d):
r01 = -(n1-n0+y)/(n0+n1+y)
t01 = 2*n0/(n0+n1+y)
t10 = 2*n1/(n0+n1+y)
r10 = -(n0-n1+y)/(n0+n1+y)
return abs(r01 - t01*t10*exp(4j*pi*d)/(1+r10*exp(4j*pi*d)))**2.0
# meshgrid for plotting
xlist = np.linspace(0.0, 0.5, 101)
ylist = np.linspace(0.0, 6.0, 101)
X, Y = np.meshgrid(xlist, ylist)
# function values on the meshgrid
Z = []
for y in ylist:
zslice = []
for d in xlist:
zslice.append(R(1.0,2.0,y,d))
Z.append(zslice)
# plot -------------------------------------
import matplotlib.pyplot as plt
plt.figure()
levels = [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]
cp = plt.contour(X, Y, Z, levels) # works
cp = plt.contourf(X, Y, Z, levels) # fails=provides defective image
plt.colorbar(cp)
plt.clabel(cp, inline=True, fontsize=10)
plt.show()
You are setting the labels to the contourf. However, they should be set to the contour.
import matplotlib.pyplot as plt
plt.figure()
levels = [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]
cp2 = plt.contour(X, Y, Z, levels)
cp = plt.contourf(X, Y, Z, levels)
plt.colorbar(cp)
plt.clabel(cp2, inline=True, fontsize=10)
plt.show()
Although the underlying logic is not completely clear, this solves the issue of strange contourf behaviour.

matplotlib: imshow a 2d array with plots of its marginal densities

How can one plot a 2d density with its marginal densities,
along the lines of
scatterplot-with-marginal-histograms-in-ggplot2
or
2D plot with histograms / marginals,
in matplotlib ?
In outline,
# I have --
A = a 2d numpy array >= 0
xdens ~ A.mean(axis=0)
ydens ~ A.mean(axis=1)
# I want --
pl.imshow( A )
pl.plot( xdens ) narrow, below A
pl.plot( ydens ) narrow, left of A, with the x y axes flipped
Added in 2017: see the lovely example of seaborn.jointplot,
also this on SO. (The question was in 2013, before seaborn.)
You can use sharex and sharey with subplots:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import gridspec
t = np.linspace(0, 31.3, 100)
f = np.linspace(0, 1000, 1000)
a = np.exp(-np.abs(f-200)/200)[:, None] * np.random.rand(t.size)
flim = (f.min(), f.max())
tlim = (t.min(), t.max())
gs = gridspec.GridSpec(2, 2, width_ratios=[1,3], height_ratios=[3,1])
ax = plt.subplot(gs[0,1])
axl = plt.subplot(gs[0,0], sharey=ax)
axb = plt.subplot(gs[1,1], sharex=ax)
ax.imshow(a, origin='lower', extent=tlim+flim, aspect='auto')
plt.xlim(tlim)
axl.plot(a.mean(1), f)
axb.plot(t, a.mean(0))
Which gives you:

Embedding small plots inside subplots in matplotlib

If you want to insert a small plot inside a bigger one you can use Axes, like here.
The problem is that I don't know how to do the same inside a subplot.
I have several subplots and I would like to plot a small plot inside each subplot.
The example code would be something like this:
import numpy as np
import matplotlib.pyplot as plt
fig = plt.figure()
for i in range(4):
ax = fig.add_subplot(2,2,i)
ax.plot(np.arange(11),np.arange(11),'b')
#b = ax.axes([0.7,0.7,0.2,0.2])
#it gives an error, AxesSubplot is not callable
#b = plt.axes([0.7,0.7,0.2,0.2])
#plt.plot(np.arange(3),np.arange(3)+11,'g')
#it plots the small plot in the selected position of the whole figure, not inside the subplot
Any ideas?
I wrote a function very similar to plt.axes. You could use it for plotting yours sub-subplots. There is an example...
import matplotlib.pyplot as plt
import numpy as np
#def add_subplot_axes(ax,rect,facecolor='w'): # matplotlib 2.0+
def add_subplot_axes(ax,rect,axisbg='w'):
fig = plt.gcf()
box = ax.get_position()
width = box.width
height = box.height
inax_position = ax.transAxes.transform(rect[0:2])
transFigure = fig.transFigure.inverted()
infig_position = transFigure.transform(inax_position)
x = infig_position[0]
y = infig_position[1]
width *= rect[2]
height *= rect[3] # <= Typo was here
#subax = fig.add_axes([x,y,width,height],facecolor=facecolor) # matplotlib 2.0+
subax = fig.add_axes([x,y,width,height],axisbg=axisbg)
x_labelsize = subax.get_xticklabels()[0].get_size()
y_labelsize = subax.get_yticklabels()[0].get_size()
x_labelsize *= rect[2]**0.5
y_labelsize *= rect[3]**0.5
subax.xaxis.set_tick_params(labelsize=x_labelsize)
subax.yaxis.set_tick_params(labelsize=y_labelsize)
return subax
def example1():
fig = plt.figure(figsize=(10,10))
ax = fig.add_subplot(111)
rect = [0.2,0.2,0.7,0.7]
ax1 = add_subplot_axes(ax,rect)
ax2 = add_subplot_axes(ax1,rect)
ax3 = add_subplot_axes(ax2,rect)
plt.show()
def example2():
fig = plt.figure(figsize=(10,10))
axes = []
subpos = [0.2,0.6,0.3,0.3]
x = np.linspace(-np.pi,np.pi)
for i in range(4):
axes.append(fig.add_subplot(2,2,i))
for axis in axes:
axis.set_xlim(-np.pi,np.pi)
axis.set_ylim(-1,3)
axis.plot(x,np.sin(x))
subax1 = add_subplot_axes(axis,subpos)
subax2 = add_subplot_axes(subax1,subpos)
subax1.plot(x,np.sin(x))
subax2.plot(x,np.sin(x))
if __name__ == '__main__':
example2()
plt.show()
You can now do this with matplotlibs inset_axes method (see docs):
from mpl_toolkits.axes_grid.inset_locator import inset_axes
inset_axes = inset_axes(parent_axes,
width="30%", # width = 30% of parent_bbox
height=1., # height : 1 inch
loc=3)
Update: As Kuti pointed out, for matplotlib version 2.1 or above, you should change the import statement to:
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
There is now also a full example showing all different options available.
From matplotlib 3.0 on, you can use matplotlib.axes.Axes.inset_axes:
import numpy as np
import matplotlib.pyplot as plt
fig, axes = plt.subplots(2,2)
for ax in axes.flat:
ax.plot(np.arange(11),np.arange(11))
ins = ax.inset_axes([0.7,0.7,0.2,0.2])
plt.show()
The difference to mpl_toolkits.axes_grid.inset_locator.inset_axes mentionned in #jrieke's answer is that this is a lot easier to use (no extra imports etc.), but has the drawback of being slightly less flexible (no argument for padding or corner locations).
source: https://matplotlib.org/examples/pylab_examples/axes_demo.html
from mpl_toolkits.axes_grid.inset_locator import inset_axes
import matplotlib.pyplot as plt
import numpy as np
# create some data to use for the plot
dt = 0.001
t = np.arange(0.0, 10.0, dt)
r = np.exp(-t[:1000]/0.05) # impulse response
x = np.random.randn(len(t))
s = np.convolve(x, r)[:len(x)]*dt # colored noise
fig = plt.figure(figsize=(9, 4),facecolor='white')
ax = fig.add_subplot(121)
# the main axes is subplot(111) by default
plt.plot(t, s)
plt.axis([0, 1, 1.1*np.amin(s), 2*np.amax(s)])
plt.xlabel('time (s)')
plt.ylabel('current (nA)')
plt.title('Subplot 1: \n Gaussian colored noise')
# this is an inset axes over the main axes
inset_axes = inset_axes(ax,
width="50%", # width = 30% of parent_bbox
height=1.0, # height : 1 inch
loc=1)
n, bins, patches = plt.hist(s, 400, normed=1)
#plt.title('Probability')
plt.xticks([])
plt.yticks([])
ax = fig.add_subplot(122)
# the main axes is subplot(111) by default
plt.plot(t, s)
plt.axis([0, 1, 1.1*np.amin(s), 2*np.amax(s)])
plt.xlabel('time (s)')
plt.ylabel('current (nA)')
plt.title('Subplot 2: \n Gaussian colored noise')
plt.tight_layout()
plt.show()